US9382239B2 - Inhibitors of c-Jun-N-terminal kinase (JNK) - Google Patents

Inhibitors of c-Jun-N-terminal kinase (JNK) Download PDF

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US9382239B2
US9382239B2 US14/358,606 US201214358606A US9382239B2 US 9382239 B2 US9382239 B2 US 9382239B2 US 201214358606 A US201214358606 A US 201214358606A US 9382239 B2 US9382239 B2 US 9382239B2
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Nathanael Gray
Tinghu Zhang
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Dana Farber Cancer Institute Inc
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Definitions

  • the MAPK (Mitogen-Activated Protein Kinase) signaling system is comprised of, at least, four distinct signaling modules defined by a core of MAP4K, MAP3K, MAP2K and MAPKs that are named after the “terminal” MAPK kinase in each pathway: ERK1/2, JNK1/2/3, p38alpha/beta, and ERK5 (Chang et al., 2001; Johnson et al., 2002; Pearson et al., 2001; and Raman et al., 2007), JNKs (c-Jun NH 2 -terminal kinase) become highly activated after cells are exposed to stress conditions such as cytokines, osmotic stress, hypoxia, and UV light, and are poorly activated by exposure to growth factors or mitogens (Derijard et al., 1994; and Pulverer et al., 1991).
  • stress conditions such as cytokines, osmotic stress, hypoxia, and UV
  • Jnk1, Jnk2, and Jnk3 that are alternatively spliced to yield approximately ten different proteins with the predominant isoforms: JNK1 and JNK2 expressed ubiquitously, and JNK3 expressed primarily in the nervous system (Derijard et al., 1994; Kallunki et al., 1994; Sluss et al., 1994; and Mohit et al., 1995).
  • JNKs are activated by phosphorylation at the activation T-loop residues Thr183/Tyr185 by the MAP2Ks: MKK4 and MKK7, and are deactivated by MAP kinase phosphatases including MKP1 and MKP5.
  • JNKs comprise a central node in the inflammatory signaling network
  • JIP which assemble signaling complexes containing MAP3K, MAP2K, and MAPKs in addition to transcription factors such as c-Jun, ATF2, and Elk1 which are phosphorylated by JNK.
  • JNKs comprise a central node in the inflammatory signaling network
  • hyperactivation of JNK signaling is a very common finding in a number of disease states including cancer, inflammatory, and neurodegenerative diseases.
  • a significant body of genetic and pharmacological evidence has been generated that suggest that inhibitors of JNK signaling may provide a promising therapeutic strategy.
  • JNK3 knockout mice exhibit amelioration of neurodegeneration in animal models of Parkinson's and Alzheimer's disease (Kyriakis et al., 2001; Zhang et al., 2005; and Hunot et al., 2004). JNK1 phosphorylates IRS-1, a key molecule in the insulin-sensing pathway which down-regulates insulin signaling, and JNK1 knockout mice are resistant to diet-induced obesity (Aguirre et al., 2000 and 2002; Hirosumi et al., 2002; and Sabio et al., 2010).
  • JNK2 often in concert with JNK1, has been implicated in the pathology of autoimmune disorders such as rheumatoid arthritis (Han et al., 2002) and asthma (Wong, W. S., 2005; Pelaia et al., 2005; Blease et al., 2003; Chialda et al., 2005); A recent study suggests that JNK2 may play a role in vascular disease and atherosclerosis as well (Osto et al., 2008). Yet, to date, no direct JNK inhibitors have been approved for use in humans.
  • one of the earliest and still most widely utilized inhibitors is the anthrapyrazolone, SP-600125 (Bennett et al., 2001) ( Figure 1) which exhibits exceptionally low specificity for JNK (Bain et al., 2007) and should only be used in combination with other approaches such as gene deletions or siRNA mediated depletion to rule-out a JNK role in a particular process (Inesta-Vaquera et al., 2010).
  • JNK inhibitors such as AS601245 (Gaillard et al., 2005) only inhibit c-Jun phosphorylation at high concentrations which is likely due to a combination of limited cell penetration, ATP concentration, and differences between biochemical and cellular sensitivities to JNK inhibitors.
  • JNKs The mitogen activated c-Jun-N-terminal kinases (JNKs, such as JNK1, JNK2, and JNK3) are key enzymes in signaling modules that transduce and integrate extracellular stimuli into coordinated cellular response.
  • Irreversible JNK inhibitors such as JNK-IN-7, were discovered to form a covalent bond with a cysteine residue conserved in JNKs.
  • Some irreversible JNK inhibitors, such as JNK-IN-8 are selective JNK inhibitors that inhibit c-Jun phosphorylation, a direct JNK substrate, in cells in a manner that was dependent on covalent modification of the conserved cysteine residue. Extensive biochemical, cellular, and pathway-based profiling were used to establish the JNK selectivity of these compounds and suggested their applicability as versatile pharmacological probes of JNK-mediated biological phenomena.
  • the present invention provides compounds of Formula (I), and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof.
  • the present invention further provides methods of using the inventive compounds, and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof, to study the inhibition of JNK and as therapeutics for the prevention and treatment of diseases associated with JNK activity.
  • the inventive compounds are used for the prevention and treatment of proliferative diseases (e.g., cancer and benign neoplasms), neurodegenerative diseases, metabolic disorders, inflammatory diseases, and cardiovascular diseases.
  • the present invention provides compounds of Formula (I):
  • Ring A, Ring B, X, L 1 , L 2 , R A , R C , R D , R E , m, n, and p are as defined herein.
  • Exemplary compounds of Formulae (I) include, but are not limited to:
  • the present invention provides pharmaceutical compositions comprising a compound of Formulae (I) and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, and prodrugs thereof, and optionally a pharmaceutically acceptable excipient.
  • the invention provides methods and compositions for the treatment of diseases of a subject.
  • the diseases being treated by the inventive methods include JNK-associated diseases. Inhibition of other therapeutic targets and their associated diseases, such as CDK7 and CDK7-associated diseases, are contemplated herein.
  • Exemplary diseases include, but are not limited to, neurodegenerative diseases, metabolic disorders, inflammatory diseases, cardiovascular diseases, and proliferative diseases (e.g., cancer and benign neoplasms).
  • the methods of the invention include administering to a subject in need of treatment of a disease a therapeutically effective amount of a compound of the present invention.
  • the compound of the present invention may be, e.g., JNK-IN-5, JNK-IN-6, JNK-IN-7, JNK-IN-8, JNK-IN-9, JNK-IN-10, JNK-IN-11, and JNK-IN-12, or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof.
  • Compounds described herein can comprise one or more asymmetric centers, and thus can exist in various isomeric forms, e.g., enantiomers and/or diastereomers.
  • the compounds described herein can be in the form of an individual enantiomer, diastereomer or geometric isomer, or can be in the form of a mixture of stereoisomers, including racemic mixtures and mixtures enriched in one or more stereoisomer.
  • Isomers can be isolated from mixtures by methods known to those skilled in the art, including chiral high pressure liquid chromatography (HPLC) and the formation and crystallization of chiral salts; or preferred isomers can be prepared by asymmetric syntheses.
  • HPLC high pressure liquid chromatography
  • C 1-6 is intended to encompass, C 1 , C 2 , C 3 , C 4 , C 5 , C 6 , C 1-6 , C 1-5 , C 1-4 , C 1-3 , C 1-2 , C 2-6 , C 2-5 , C 2-4 , C 2-3 , C 3-6 , C 3-5 , C 3-4 , C 4-6 , C 4-5 , and C 5-6 .
  • hydrocarbon chain refers to a substituted or unsubstituted divalent alkyl, alkenyl, or alkynyl group.
  • a hydrocarbon chain includes at least one chain, each node (“carbon unit”) of which including at least one carbon atom, between the two radicals of the hydrocarbon chain.
  • hydrocarbon chain —C A H(C B H 2 C C H 3 )— includes only one carbon unit C A .
  • C x hydrocarbon chain wherein x is a positive integer, refers to a hydrocarbon chain that includes x number of carbon unit(s) between the two radicals of the hydrocarbon chain. If there is more than one possible value of x, the smallest possible value of x is used for the definition of the hydrocarbon chain.
  • —CH(C 2 H 5 )— is a C 1 hydrocarbon chain
  • a hydrocarbon chain is a C 3 hydrocarbon chain.
  • a hydrocarbon chain may be saturated (e.g., —(CH 2 ) 4 —).
  • a hydrocarbon chain may also be unsaturated and include one or more C ⁇ C and/or C ⁇ C bonds anywhere in the hydrocarbon chain. For instance, —CH ⁇ CH(CH 2 ) 2 —, —CH 2 C ⁇ C ⁇ C—H 2 —, and —C ⁇ C—CH ⁇ CH— are all examples of a unsubstituted and unsaturated hydrocarbon chain.
  • the hydrocarbon chain is unsubstituted (e.g., —(CH 2 ) 4 —). In certain embodiments, the hydrocarbon chain is substituted (e.g., —CH(C 2 H 5 )— and —CF 2 —). Any two substituents on the hydrocarbon chain may be joined to form an optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl ring. For instance,
  • Alkyl refers to a radical of a straight-chain or branched saturated hydrocarbon group having from 1 to 20 carbon atoms (“C 1-20 alkyl”). In some embodiments, an alkyl group has 1 to 10 carbon atoms (“C 1-10 alkyl”). In some embodiments, an alkyl group has 1 to 9 carbon atoms (“C 1-9 alkyl”). In some embodiments, an alkyl group has 1 to 8 carbon atoms (“C 1-8 alkyl”). In some embodiments, an alkyl group has 1 to 7 carbon atoms (“C 1-7 alkyl”). In some embodiments, an alkyl group has 1 to 6 carbon atoms (“C 1-6 alkyl”).
  • an alkyl group has 1 to 5 carbon atoms (“C 1-5 alkyl”). In some embodiments, an alkyl group has 1 to 4 carbon atoms (“C 1-4 alkyl”). In some embodiments, an alkyl group has 1 to 3 carbon atoms (“C 1-3 alkyl”). In some embodiments, an alkyl group has 1 to 2 carbon atoms (“C 1-2 alkyl”). In some embodiments, an alkyl group has 1 carbon atom (“C 1 alkyl”). In some embodiments, an alkyl group has 2 to 6 carbon atoms (“C 2-6 alkyl”).
  • C 1-6 alkyl groups include methyl (C 1 ), ethyl (C 2 ), n-propyl (C 3 ), isopropyl (C 3 ), n-butyl (C 4 ), tert-butyl (C 4 ), sec-butyl (C 4 ), iso-butyl (C 4 ), n-pentyl (C 5 ), 3-pentanyl (C 5 ), amyl (C 5 ), neopentyl (C 5 ), 3-methyl-2-butanyl (C 5 ), tertiary amyl (C 5 ), and n-hexyl (C 6 ).
  • alkyl groups include n-heptyl (C 7 ), n-octyl (C 8 ) and the like. Unless otherwise specified, each instance of an alkyl group is independently optionally substituted, i.e., unsubstituted (an “unsubstituted alkyl”) or substituted (a “substituted alkyl”) with one or more substituents. In certain embodiments, the alkyl group is unsubstituted C 1-10 alkyl (e.g., —CH 3 ). In certain embodiments, the alkyl group is substituted C 1-10 alkyl.
  • Alkenyl refers to a radical of a straight-chain or branched hydrocarbon group having from 2 to 20 carbon atoms, one or more carbon-carbon double bonds, and no triple bonds (“C 2-20 alkenyl”). In some embodiments, an alkenyl group has 2 to 10 carbon atoms (“C 2-10 alkenyl”). In some embodiments, an alkenyl group has 2 to 9 carbon atoms (“C 2-9 alkenyl”). In some embodiments, an alkenyl group has 2 to 8 carbon atoms (“C 2-8 alkenyl”). In some embodiments, an alkenyl group has 2 to 7 carbon atoms (“C 2-7 alkenyl”).
  • an alkenyl group has 2 to 6 carbon atoms (“C 2-6 alkenyl”). In some embodiments, an alkenyl group has 2 to 5 carbon atoms (“C 2-5 alkenyl”). In some embodiments, an alkenyl group has 2 to 4 carbon atoms (“C 2-4 alkenyl”). In some embodiments, an alkenyl group has 2 to 3 carbon atoms (“C 2-3 alkenyl”). In some embodiments, an alkenyl group has 2 carbon atoms (“C 2 alkenyl”). The one or more carbon carbon double bonds can be internal (such as in 2-butenyl) or terminal (such as in 1-butenyl).
  • Examples of C 2-4 alkenyl groups include ethenyl (C 2 ), 1-propenyl (C 3 ), 2-propenyl (C 3 ), 1-butenyl (C 4 ), 2-butenyl (C 4 ), butadienyl (C 4 ), and the like.
  • Examples of C 2-6 alkenyl groups include the aforementioned C 2-4 alkenyl groups as well as pentenyl (C 5 ), pentadienyl (C 5 ), hexenyl (C 6 ), and the like. Additional examples of alkenyl include heptenyl (C 7 ), octenyl (C 8 ), octatrienyl (C 8 ), and the like.
  • each instance of an alkenyl group is independently optionally substituted, i.e., unsubstituted (an “unsubstituted alkenyl”) or substituted (a “substituted alkenyl”) with one or more substituents.
  • the alkenyl group is unsubstituted C 2-10 alkenyl.
  • the alkenyl group is substituted C 2-10 alkenyl.
  • Alkynyl refers to a radical of a straight-chain or branched hydrocarbon group having from 2 to 20 carbon atoms, one or more carbon-carbon triple bonds, and optionally one or more double bonds (“C 2-20 alkynyl”).
  • an alkynyl group has 2 to 10 carbon atoms (“C 2-10 alkynyl”).
  • an alkynyl group has 2 to 9 carbon atoms (“C 2-9 alkynyl”).
  • an alkynyl group has 2 to 8 carbon atoms (“C 2-8 alkynyl”).
  • an alkynyl group has 2 to 7 carbon atoms (“C 2-7 alkynyl”).
  • an alkynyl group has 2 to 6 carbon atoms (“C 2-6 alkynyl”). In some embodiments, an alkynyl group has 2 to 5 carbon atoms (“C 2-5 alkynyl”). In some embodiments, an alkynyl group has 2 to 4 carbon atoms (“C 2-4 alkynyl”). In some embodiments, an alkynyl group has 2 to 3 carbon atoms (“C 2-3 alkynyl”). In some embodiments, an alkynyl group has 2 carbon atoms (“C 2 alkynyl”). The one or more carbon-carbon triple bonds can be internal (such as in 2-butynyl) or terminal (such as in 1-butynyl).
  • Examples of C 2-4 alkynyl groups include, without limitation, ethynyl (C 2 ), 1-propynyl (C 3 ), 2-propynyl (C 3 ), 1-butynyl (C 4 ), 2-butynyl (C 4 ), and the like.
  • Examples of C 2-6 alkenyl groups include the aforementioned C 2-4 alkynyl groups as well as pentynyl (C 5 ), hexynyl (C 6 ), and the like. Additional examples of alkynyl include heptynyl (C 7 ), octynyl (C 8 ), and the like.
  • each instance of an alkynyl group is independently optionally substituted, i.e., unsubstituted (an “unsubstituted alkynyl”) or substituted (a “substituted alkynyl”) with one or more substituents.
  • the alkynyl group is unsubstituted C 2-10 alkynyl.
  • the alkynyl group is substituted C 2-10 alkynyl.
  • Carbocyclyl or “carbocyclic” refers to a radical of a non-aromatic cyclic hydrocarbon group having from 3 to 10 ring carbon atoms (“C 3-10 carbocyclyl”) and zero heteroatoms in the non-aromatic ring system.
  • a carbocyclyl group has 3 to 8 ring carbon atoms (“C 3-8 carbocyclyl”).
  • a carbocyclyl group has 3 to 6 ring carbon atoms (“C 3-6 carbocyclyl”).
  • a carbocyclyl group has 3 to 6 ring carbon atoms (“C 3-6 carbocyclyl”).
  • a carbocyclyl group has 5 to 10 ring carbon atoms (“C 5-10 carbocyclyl”).
  • Exemplary C 3-6 carbocyclyl groups include, without limitation, cyclopropyl (C 3 ), cyclopropenyl (C 3 ), cyclobutyl (C 4 ), cyclobutenyl (C 4 ), cyclopentyl (C 5 ), cyclopentenyl (C 5 ), cyclohexyl (C 6 ), cyclohexenyl (C 6 ), cyclohexadienyl (C 6 ), and the like.
  • Exemplary C 3-8 carbocyclyl groups include, without limitation, the aforementioned C 3-6 carbocyclyl groups as well as cycloheptyl (C 7 ), cycloheptenyl (C 7 ), cycloheptadienyl (C 7 ), cycloheptatrienyl (C 7 ), cyclooctyl (C 8 ), cyclooctenyl (C 8 ), bicyclo[2.2.1]heptanyl (C 7 ), bicyclo[2.2.2]octanyl (C 8 ), and the like.
  • Exemplary C 3-10 carbocyclyl groups include, without limitation, the aforementioned C 3-8 carbocyclyl groups as well as cyclononyl (C 9 ), cyclononenyl (C 9 ), cyclodecyl (C 10 ), cyclodecenyl (C 10 ), octahydro-1H-indenyl (C 9 ), decahydronaphthalenyl (C 10 ), spiro[4.5]decanyl (C 10 ), and the like.
  • the carbocyclyl group is either monocyclic (“monocyclic carbocyclyl”) or contain a fused, bridged or spiro ring system such as a bicyclic system (“bicyclic carbocyclyl”) and can be saturated or can be partially unsaturated.
  • “Carbocyclyl” also includes ring systems wherein the carbocyclic ring, as defined above, is fused with one or more aryl or heteroaryl groups wherein the point of attachment is on the carbocyclic ring, and in such instances, the number of carbons continue to designate the number of carbons in the carbocyclic ring system.
  • each instance of a carbocyclyl group is independently optionally substituted, i.e., unsubstituted (an “unsubstituted carbocyclyl”) or substituted (a “substituted carbocyclyl”) with one or more substituents.
  • the carbocyclyl group is unsubstituted C 3-10 carbocyclyl.
  • the carbocyclyl group is a substituted C 3-10 carbocyclyl.
  • “carbocyclyl” is a monocyclic, saturated carbocyclyl group having from 3 to 10 ring carbon atoms (“C 3-10 cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 8 ring carbon atoms (“C 3-8 cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 6 ring carbon atoms (“C 3-6 cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 6 ring carbon atoms (“C 5-6 cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 10 ring carbon atoms (“C 5-10 cycloalkyl”).
  • C 5-6 cycloalkyl groups include cyclopentyl (C 5 ) and cyclohexyl (C 5 ).
  • Examples of C 3-6 cycloalkyl groups include the aforementioned C 5-6 cycloalkyl groups as well as cyclopropyl (C 3 ) and cyclobutyl (C 4 ).
  • Examples of C 3-8 cycloalkyl groups include the aforementioned C 3-6 cycloalkyl groups as well as cycloheptyl (C 7 ) and cyclooctyl (C 8 ).
  • each instance of a cycloalkyl group is independently unsubstituted (an “unsubstituted cycloalkyl”) or substituted (a “substituted cycloalkyl”) with one or more substituents.
  • the cycloalkyl group is unsubstituted C 3-10 cycloalkyl.
  • the cycloalkyl group is substituted C 3-10 cycloalkyl.
  • Heterocyclyl or “heterocyclic” refers to a radical of a 3- to 10-membered nonaromatic ring system having ring carbon atoms and 1 to 4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, sulfur, boron, phosphorus, and silicon (“3-10 membered heterocyclyl”).
  • the point of attachment can be a carbon or nitrogen atom, as valency permits.
  • a heterocyclyl group can either be monocyclic (“monocyclic heterocyclyl”) or a fused, bridged or spiro ring system such as a bicyclic system (“bicyclic heterocyclyl”), and can be saturated or can be partially unsaturated.
  • Heterocyclyl bicyclic ring systems can include one or more heteroatoms in one or both rings.
  • Heterocyclyl also includes ring systems wherein the heterocyclic ring, as defined above, is fused with one or more carbocyclyl groups wherein the point of attachment is either on the carbocyclyl or heterocyclic ring, or ring systems wherein the heterocyclic ring, as defined above, is fused with one or more aryl or heteroaryl groups, wherein the point of attachment is on the heterocyclic ring, and in such instances, the number of ring members continue to designate the number of ring members in the heterocyclic ring system.
  • each instance of heterocyclyl is independently optionally substituted, i.e., unsubstituted (an “unsubstituted heterocyclyl”) or substituted (a “substituted heterocyclyl”) with one or more substituents.
  • the heterocyclyl group is unsubstituted 3-10 membered heterocyclyl. In certain embodiments, the heterocyclyl group is substituted 3-10 membered heterocyclyl.
  • a heterocyclyl group is a 5-10 membered non aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, sulfur, boron, phosphorus, and silicon (“5-10 membered heterocyclyl”).
  • a heterocyclyl group is a 5-8 membered nonaromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-8 membered heterocyclyl”).
  • a heterocyclyl group is a 5-6 membered nonaromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-6 membered heterocyclyl”).
  • the 5-6 membered heterocyclyl has 1-3 ring heteroatoms selected from nitrogen, oxygen, and sulfur.
  • the 5-6 membered heterocyclyl has 1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur.
  • the 5-6 membered heterocyclyl has one ring heteroatom selected from nitrogen, oxygen, and sulfur.
  • Exemplary 3-membered heterocyclyl groups containing one hetero atom include, without limitation, azirdinyl, oxiranyl, thiorenyl.
  • Exemplary 4-membered heterocyclyl groups containing one heteroatom include, without limitation, azetidinyl, oxetanyl and thietanyl.
  • Exemplary 5-membered heterocyclyl groups containing one heteroatom include, without limitation, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothiophenyl, dihydrothiophenyl, pyrrolidinyl, dihydropyrrolyl and pyrrolyl-2,5-dione.
  • Exemplary 5-membered heterocyclyl groups containing two heteroatoms include, without limitation, dioxolanyl, oxasulfuranyl, disulfuranyl, and oxazolidin-2-one.
  • Exemplary 5-membered heterocyclyl groups containing three heteroatoms include, without limitation, triazolinyl, oxadiazolinyl, and thiadiazolinyl.
  • Exemplary 6-membered heterocyclyl groups containing one heteroatom include, without limitation, piperidinyl, tetrahydropyranyl, dihydropyridinyl, and thianyl.
  • Exemplary 6-membered heterocyclyl groups containing two heteroatoms include, without limitation, piperazinyl, morpholinyl, dithianyl, dioxanyl. Exemplary 6-membered heterocyclyl groups containing two heteroatoms include, without limitation, triazinanyl. Exemplary 7-membered heterocyclyl groups containing one heteroatom include, without limitation, azepanyl, oxepanyl and thiepanyl. Exemplary 8-membered heterocyclyl groups containing one heteroatom include, without limitation, azocanyl, oxecanyl and thiocanyl.
  • Exemplary 5-membered heterocyclyl groups fused to a C 6 aryl ring include, without limitation, indolinyl, isoindolinyl, dihydrobenzofuranyl, dihydrobenzothienyl, benzoxazolinonyl, and the like.
  • Exemplary 6-membered heterocyclyl groups fused to an aryl ring include, without limitation, tetrahydroquinolinyl, tetrahydroisoquinolinyl, and the like.
  • Aryl refers to a radical of a monocyclic or polycyclic (e.g., bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 ⁇ electrons shared in a cyclic array) having 6-14 ring carbon atoms and zero heteroatoms provided in the aromatic ring system (“C 6-14 aryl”).
  • an aryl group has six ring carbon atoms (“C 6 aryl”; e.g., phenyl).
  • an aryl group has ten ring carbon atoms (“C 10 aryl”; e.g., naphthyl such as 1-naphthyl and 2-naphthyl).
  • an aryl group has fourteen ring carbon atoms (“C 14 aryl”; e.g., anthracyl).
  • Aryl also includes ring systems wherein the aryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the radical or point of attachment is on the aryl ring, and in such instances, the number of carbon atoms continue to designate the number of carbon atoms in the aryl ring system.
  • each instance of an aryl group is independently optionally substituted, i.e., unsubstituted (an “unsubstituted aryl”) or substituted (a “substituted aryl”) with one or more substituents.
  • the aryl group is unsubstituted C 6-14 aryl.
  • the aryl group is substituted C 6-14 aryl.
  • Alkyl is a subset of alkyl and aryl, as defined herein, and refers to an optionally substituted alkyl group substituted by an optionally substituted aryl group.
  • Heteroaryl refers to a radical of a 5-10 membered monocyclic or bicyclic 4n+2 aromatic ring system (e.g., having 6 or 10 ⁇ electrons shared in a cyclic array) having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen and sulfur (“5-10 membered heteroaryl”).
  • heteroaryl groups that contain one or more nitrogen atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits.
  • Heteroaryl bicyclic ring systems can include one or more heteroatoms in one or both rings.
  • Heteroaryl includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the point of attachment is on the heteroaryl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heteroaryl ring system. “Heteroaryl” also includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more aryl groups wherein the point of attachment is either on the aryl or heteroaryl ring, and in such instances, the number of ring members designates the number of ring members in the fused (aryl/heteroaryl) ring system.
  • Bicyclic heteroaryl groups wherein one ring does not contain a heteroatom e.g., indolyl, quinolinyl, carbazolyl, and the like
  • the point of attachment can be on either ring, i.e., either the ring bearing a heteroatom (e.g., 2-indolyl) or the ring that does not contain a heteroatom (e.g., 5-indolyl).
  • a heteroaryl group is a 5-10 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-10 membered heteroaryl”).
  • a heteroaryl group is a 5-8 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-8 membered heteroaryl”).
  • a heteroaryl group is a 5-6 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-6 membered heteroaryl”).
  • the 5-6 membered heteroaryl has 1-3 ring heteroatoms selected from nitrogen, oxygen, and sulfur.
  • the 5-6 membered heteroaryl has 1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur.
  • the 5-6 membered heteroaryl has 1 ring heteroatom selected from nitrogen, oxygen, and sulfur.
  • each instance of a heteroaryl group is independently optionally substituted, i.e., unsubstituted (an “unsubstituted heteroaryl”) or substituted (a “substituted heteroaryl”) with one or more substituents.
  • the heteroaryl group is unsubstituted 5-14 membered heteroaryl. In certain embodiments, the heteroaryl group is substituted 5-14 membered heteroaryl.
  • Exemplary 5-membered heteroaryl groups containing one heteroatom include, without limitation, pyrrolyl, furanyl and thiophenyl.
  • Exemplary 5-membered heteroaryl groups containing two heteroatoms include, without limitation, imidazolyl, pyrazolyl, oxazolyl, isoxazolyl, thiazolyl, and isothiazolyl.
  • Exemplary 5-membered heteroaryl groups containing three heteroatoms include, without limitation, triazolyl, oxadiazolyl, and thiadiazolyl.
  • Exemplary 5-membered heteroaryl groups containing four heteroatoms include, without limitation, tetrazolyl.
  • Exemplary 6-membered heteroaryl groups containing one heteroatom include, without limitation, pyridinyl.
  • Exemplary 6-membered heteroaryl groups containing two heteroatoms include, without limitation, pyridazinyl, pyrimidinyl, and pyrazinyl.
  • Exemplary 6-membered heteroaryl groups containing three or four heteroatoms include, without limitation, triazinyl and tetrazinyl, respectively.
  • Exemplary 7-membered heteroaryl groups containing one heteroatom include, without limitation, azepinyl, oxepinyl, and thiepinyl.
  • Exemplary 5,6-bicyclic heteroaryl groups include, without limitation, indolyl, isoindolyl, indazolyl, benzotriazolyl, benzothiophenyl, isobenzothiophenyl, benzofuranyl, benzoisofuranyl, benzimidazolyl, benzoxazolyl, benzisoxazolyl, benzoxadiazolyl, benzthiazolyl, benzisothiazolyl, benzthiadiazolyl, indolizinyl, and purinyl.
  • Exemplary 6,6-bicyclic heteroaryl groups include, without limitation, naphthyridinyl, pteridinyl, quinolinyl, isoquinolinyl, cinnolinyl, quinoxalinyl, phthalazinyl, and quinazolinyl.
  • Heteroaralkyl is a subset of alkyl and heteroaryl, as defined herein, and refers to an optionally substituted alkyl group substituted by an optionally substituted heteroaryl group.
  • Partially unsaturated refers to a group that includes at least one double or triple bond.
  • a “partially unsaturated” ring system is further intended to encompass rings having multiple sites of unsaturation, but is not intended to include aromatic groups (e.g., aryl or heteroaryl groups) as herein defined.
  • aromatic groups e.g., aryl or heteroaryl groups
  • saturated refers to a group that does not contain a double or triple bond, i.e., contains all single bonds.
  • Alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl groups, as defined herein, which are divalent bridging groups are further referred to using the suffix ene, e.g., alkylene, alkenylene, alkynylene, carbocyclylene, heterocyclylene, arylene, and heteroarylene.
  • Alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl groups, as defined herein, are optionally substituted (e.g., “substituted” or “unsubstituted” alkyl, “substituted” or “unsubstituted” alkenyl, “substituted” or “unsubstituted” alkynyl, “substituted” or “unsubstituted” carbocyclyl, “substituted” or “unsubstituted” heterocyclyl, “substituted” or “unsubstituted” aryl or “substituted” or “unsubstituted” heteroaryl group).
  • substituted means that at least one hydrogen present on a group (e.g., a carbon or nitrogen atom) is replaced with a permissible substituent, e.g., a substituent which upon substitution results in a stable compound, e.g., a compound which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, or other reaction.
  • a “substituted” group has a substituent at one or more substitutable positions of the group, and when more than one position in any given structure is substituted, the substituent is either the same or different at each position.
  • substituted is contemplated to include substitution with all permissible substituents of organic compounds, any of the substituents described herein that results in the formation of a stable compound.
  • the present invention contemplates any and all such combinations in order to arrive at a stable compound.
  • heteroatoms such as nitrogen may have hydrogen substituents and/or any suitable substituent as described herein which satisfy the valencies of the heteroatoms and results in the formation of a stable moiety.
  • Exemplary carbon atom substituents include, but are not limited to, halogen, —CN, —NO 2 , —N 3 , —SO 2 H, —SO 3 H, —OH, —OR aa , —ON(R bb ) 2 , —N(R bb ) 2 , —N(R bb ) 3 + X ⁇ , —N(OR cc )R bb , —SH, —SR aa , —SSR cc , —C( ⁇ O)R aa , —CO 2 H, —CHO, —C(OR cc ) 2 , —CO 2 R aa , —OC( ⁇ O)R aa , —OCO 2 R aa , —C( ⁇ O)N(R bb ) 2 , —OC( ⁇ O)N(R bb ) 2 , —NR bb C
  • each instance of R aa is, independently, selected from C 1-10 alkyl, C 1-10 perhaloalkyl, C 2-10 alkenyl, C 2-10 alkynyl, C 3-10 carbocyclyl, 3-14 membered heterocyclyl, C 6-14 aryl, and 5-14 membered heteroaryl, or two R aa groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R dd groups;
  • each instance of R bb is, independently, selected from hydrogen, —OH, —OR aa , —N(R cc ) 2 , —CN, —C( ⁇ O)R aa , —C( ⁇ O)N(R cc ) 2 , —CO 2 R aa , —SO 2 R aa , —C( ⁇ NR cc )OR aa , —C( ⁇ NR cc )N(R cc ) 2 , —SO 2 N(R cc ) 2 , —SO 2 R cc , —SO 2 OR cc , —SOR aa , —C( ⁇ S)N(R cc ) 2 , —C( ⁇ O)SR cc , —C( ⁇ S)SR cc , —P( ⁇ O) 2 R aa , —P( ⁇ O)(R aa ) 2 ,
  • each instance of R cc is, independently, selected from hydrogen, C 1-10 alkyl, C 1-10 perhaloalkyl, C 2-10 alkenyl, C 2-10 alkynyl, C 3-10 carbocyclyl, 3-14 membered heterocyclyl, C 6-14 aryl, and 5-14 membered heteroaryl, or two R cc groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R dd groups;
  • each instance of R dd is, independently, selected from halogen, —CN, —NO 2 , —N 3 , —SO 2 H, —SO 3 H, —OH, —OR ee , —ON(R ff ) 2 , —N(R ff ) 2 , —N(R ff ) 3 + X ⁇ , —N(OR ee )R ff , —SH, —SR ee , —SSR ee , —C( ⁇ O)R ee , —CO 2 H, —CO 2 R ee , —OC( ⁇ O)R ee , —OCO 2 R ee , —C( ⁇ O)N(R ff ) 2 , —OC( ⁇ O)N(R ff ) 2 , —NR ff C( ⁇ O)R ee , —NR ff CO 2 R
  • each instance of R ee is, independently, selected from C 1-6 alkyl, C 1-6 perhaloalkyl, C 2-6 alkenyl, C 2-6 alkynyl, C 3-10 carbocyclyl, C 6-10 aryl, 3-10 membered heterocyclyl, and 3-10 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R gg groups;
  • each instance of R ff is, independently, selected from hydrogen, C 1-6 alkyl, C 1-6 perhaloalkyl, C 2-6 alkenyl, C 2-6 alkynyl, C 3-10 carbocyclyl, 3-10 membered heterocyclyl, C 6-10 aryl and 5-10 membered heteroaryl, or two R ff groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R gg groups; and
  • each instance of R gg is, independently, halogen, —CN, —NO 2 , —N 3 , —SO 2 H, —SO 3 H, —OH, —OC 1-6 alkyl, —ON(C 1-6 alkyl) 2 , —N(C 1-6 alkyl) 2 , —N(C 1-6 alkyl) 3 + X ⁇ , —NH(C 1-6 alkyl) 2 + X ⁇ , —NH 2 (C 1-6 alkyl) + X ⁇ , —NH 3 + X ⁇ , —N(OC 1-6 alkyl)(C 1-6 alkyl), —N(OH)(C 1-6 alkyl), —NH(OH), —SH, —SC 1-6 alkyl, —SS(C 1-6 alkyl), —C( ⁇ O)(C 1-6 alkyl), —CO 2 H, —CO 2 (C 1-6 alkyl), —OC( ⁇ O)
  • a “counterion” or “anionic counterion” is a negatively charged group associated with a cationic quaternary amino group in order to maintain electronic neutrality.
  • exemplary counterions include halide ions (e.g., F ⁇ , Cl ⁇ , Br ⁇ , I ⁇ ), NO 3 ⁇ , ClO 4 ⁇ , OH ⁇ , H 2 PO 4 ⁇ , HSO 4 ⁇ , sulfonate ions (e.g., methanesulfonate, trifluoromethanesulfonate, p-toluenesulfonate, benzenesulfonate, 10-camphor sulfonate, naphthalene-2-sulfonate, naphthalene-1-sulfonic acid-5-sulfonate, ethan-1-sulfonic acid-2-sulfonate, and the like), and carboxylate ions (e.g., acetate
  • Halo or “halogen” refers to fluorine (fluoro, —F), chlorine (chloro, —Cl), bromine (bromo, —Br), or iodine (iodo, —I).
  • “Acyl” as used herein refers to a moiety selected from the group consisting of —C( ⁇ O)R aa , —CHO, —CO 2 R aa , —C( ⁇ O)N(R bb ) 2 , —C( ⁇ NR bb )R aa , —C( ⁇ NR bb )OR aa , —C( ⁇ NR bb )N(R bb ) 2 , —C( ⁇ O)NR bb SO 2 R aa , —C( ⁇ S)N(R bb ) 2 , —C( ⁇ O)SR aa , or —C( ⁇ S)SR aa , wherein R aa and R bb are as defined herein.
  • Nitrogen atoms can be substituted or unsubstituted as valency permits, and include primary, secondary, tertiary, and quaternary nitrogen atoms.
  • Exemplary nitrogen atom substitutents include, but are not limited to, hydrogen, —OH, —OR aa , —N(R cc ) 2 , —CN, —C( ⁇ O)R aa , —C( ⁇ O)N(R cc ) 2 , —CO 2 R aa , —SO 2 R aa , —C( ⁇ NR bb )R aa , —C( ⁇ NR cc )OR aa , —C( ⁇ NR cc )N(R cc ) 2 , —SO 2 N(R cc ) 2 , —SO 2 R cc , —SO 2 OR cc , —SOR aa , —C( ⁇ S)N(
  • the substituent present on a nitrogen atom is a nitrogen protecting group (also referred to as an amino protecting group).
  • Nitrogen protecting groups include, but are not limited to, —OH, —OR aa , —N(R cc ) 2 , —C( ⁇ O)R aa , —C( ⁇ O)N(R cc ) 2 , —CO 2 R aa , —SO 2 R aa , —C( ⁇ NR cc )R aa , —C( ⁇ NR cc )OR aa , —C( ⁇ NR cc )N(R cc ) 2 , —SO 2 N(R cc ) 2 , —SO 2 R cc , —SO 2 OR cc , —SOR aa , —C( ⁇ S)N(R cc ) 2 , —C( ⁇ O)SR cc , —C(C(
  • Nitrogen protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis , T. W. Greene and P. G. M. Wuts, 3 rd edition, John Wiley & Sons, 1999, incorporated herein by reference.
  • nitrogen protecting groups such as amide groups (e.g., —C( ⁇ O)R aa ) include, but are not limited to, formamide, acetamide, chloroacetamide, trichloroacetamide, trifluoroacetamide, phenylacetamide, 3-phenylpropanamide, picolinamide, 3-pyridylcarboxamide, N-benzoylphenylalanyl derivative, benzamide, p-phenylbenzamide, o-nitophenylacetamide, o-nitrophenoxyacetamide, acetoacetamide, (N′-dithiobenzyloxyacylamino)acetamide, 3-(p-hydroxyphenyl)propanamide, 3-(o-nitrophenyl)propanamide, 2-methyl-2-(o-nitrophenoxy)propanamide, 2-methyl-2-(o-phenylazophenoxy)propanamide, 4-chlorobutanamide, 3-methyl-3-nitrobutanamide, o-nitro
  • Nitrogen protecting groups such as carbamate groups include, but are not limited to, methyl carbamate, ethyl carbamante, 9-fluorenylmethyl carbamate (Fmoc), 9-(2-sulfo)fluorenylmethyl carbamate, 9-(2,7-dibromo)fluoroenylmethyl carbamate, 2,7-di-t-butyl-[9-(10,10-dioxo-10,10,10,10-tetrahydrothioxanthyl)]methyl carbamate (DBD-Tmoc), 4-methoxyphenacyl carbamate (Phenoc), 2,2,2-trichloroethyl carbamate (Troc), 2-trimethylsilylethyl carbamate (Teoc), 2-phenylethyl carbamate (hZ), 1-(1-adamantyl)-1-methylethyl carbamate
  • Nitrogen protecting groups such as sulfonamide groups include, but are not limited to, p-toluenesulfonamide (Ts), benzenesulfonamide, 2,3,6,-trimethyl-4-methoxybenzenesulfonamide (Mtr), 2,4,6-trimethoxybenzenesulfonamide (Mtb), 2,6-dimethyl-4-methoxybenzenesulfonamide (Pme), 2,3,5,6-tetramethyl-4-methoxybenzenesulfonamide (Mte), 4-methoxybenzenesulfonamide (Mbs), 2,4,6-trimethylbenzenesulfonamide (Mts), 2,6-dimethoxy-4-methylbenzenesulfonamide (iMds), 2,2,5,7,8-pentamethylchroman-6-sulfonamide (Pmc), methanesulfonamide
  • Ts p-toluenesulfonamide
  • nitrogen protecting groups include, but are not limited to, benzoyl (Bz), phenothiazinyl-(10)-acyl derivative, N′-p-toluenesulfonylaminoacyl derivative, N′-phenylaminothioacyl derivative, N-benzoylphenylalanyl derivative, N-acetylmethionine derivative, 4,5-diphenyl-3-oxazolin-2-one, N-phthalimide, N-dithiasuccinimide (Dts), N-2,3-diphenylmaleimide, N-2,5-dimethylpyrrole, N-1,1,4,4-tetramethyldisilylazacyclopentane adduct (STABASE), 5-substituted 1,3-dimethyl-1,3,5-triazacyclohexan-2-one, 5-substituted 1,3-dibenzyl-1,3,5-triazacyclohexan-2-one, 1-substit
  • the substituent present on an oxygen atom is an oxygen protecting group (also referred to as a hydroxyl protecting group).
  • Oxygen protecting groups include, but are not limited to, —R aa , —N(R bb ) 2 , —C( ⁇ O)SR aa , —C( ⁇ O)R aa , —CO 2 R aa , —C( ⁇ O)N(R bb ) 2 , —C( ⁇ NR bb )R aa , —C( ⁇ NR bb )OR aa , —C( ⁇ NR bb )N(R bb ) 2 , —S( ⁇ O)R aa , —SO 2 R aa , —Si(R aa ) 3 , —P(R cc ) 2 , —P(R cc ) 3 , —P( ⁇ O) 2 R aa ,
  • Oxygen protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis , T. W. Greene and P. G. M. Wuts, 3 rd edition, John Wiley & Sons, 1999, incorporated herein by reference.
  • oxygen protecting groups include, but are not limited to, methyl, methoxylmethyl (MOM), methylthiomethyl (MTM), t-butylthiomethyl, (phenyldimethylsilyl)methoxymethyl (SMOM), benzyloxymethyl (BOM), p-methoxybenzyloxymethyl (PMBM), (4-methoxyphenoxy)methyl (p-AOM), guaiacolmethyl (GUM), t-butoxymethyl, 4-pentenyloxymethyl (POM), siloxymethyl, 2-methoxyethoxymethyl (MEM), 2,2,2-trichloroethoxymethyl, bis(2-chloroethoxy)methyl, 2-(trimethylsilyl)ethoxymethyl (SEMOR), tetrahydropyranyl (THP), 3-bromotetrahydropyranyl, tetrahydrothiopyranyl, 1-methoxycyclohexyl, 4-methoxytetrahydropyranyl (MTHP), 4-meth
  • the substituent present on an sulfur atom is an sulfur protecting group (also referred to as a thiol protecting group).
  • Sulfur protecting groups include, but are not limited to, —R aa , —N(R bb ) 2 , —C( ⁇ O)SR aa , —C( ⁇ O)R aa , —CO 2 R aa , —C( ⁇ O)N(R bb ) 2 , —C( ⁇ NR bb )R aa , —C( ⁇ NR bb )OR aa , —C( ⁇ NR bb )N(R bb ) 2 , —S( ⁇ O)R aa , SO 2 R aa , —Si(R aa ) 3 , —P(R cc ) 2 , —P(R cc ) 3 , —P( ⁇ O) 2 R aa , —
  • Sulfur protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis , T. W. Greene and P. G. M. Wuts, 3 rd edition, John Wiley & Sons, 1999, incorporated herein by reference.
  • leaving group is given its ordinary meaning in the art of synthetic organic chemistry and refers to an atom or a group capable of being displaced by a nucleophile.
  • suitable leaving groups include, but are not limited to, halogen (such as F, Cl, Br, or I (iodine)), alkoxycarbonyloxy, aryloxycarbonyloxy, alkanesulfonyloxy, arenesulfonyloxy, alkyl-carbonyloxy (e.g., acetoxy), arylcarbonyloxy, aryloxy, methoxy, N,O-dimethylhydroxylamino, pixyl, and haloformates.
  • the leaving group is a sulfonic acid ester, such as toluenesulfonate (tosylate, —OTs), methanesulfonate (mesylate, —OMs), p-bromobenzenesulfonyloxy (brosylate, —OBs), or trifluoromethanesulfonate (triflate, —OTf).
  • the leaving group is a brosylate, such as p-bromobenzenesulfonyloxy.
  • the leaving group is a nosylate, such as 2-nitrobenzenesulfonyloxy.
  • the leaving group is a sulfonate-containing group. In some embodiments, the leaving group is a tosylate group.
  • the leaving group may also be a phosphineoxide (e.g., formed during a Mitsunobu reaction) or an internal leaving group such as an epoxide or cyclic sulfate.
  • Other non-limiting examples of leaving groups are water, ammonia, alcohols, ether moieties, thioether moieties, zinc halides, magnesium moieties, diazonium salts, and copper moieties.
  • the term “pharmaceutically acceptable salt” refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio.
  • Pharmaceutically acceptable salts are well known in the art. For example, Berge et al., describe pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences, 1977, 66, 1-19, incorporated herein by reference.
  • Pharmaceutically acceptable salts of the compounds of this invention include those derived from suitable inorganic and organic acids and bases.
  • Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid, and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, or malonic acid or by using other methods known in the art such as ion exchange.
  • inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid, and perchloric acid
  • organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, or malonic acid or by using other methods known in the art such as ion exchange.
  • salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxyethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, per
  • Salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium and N+(C1-4alkyl)4 salts.
  • Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like.
  • Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, loweralkyl sulfonate, and aryl sulfonate.
  • Solidvate refers to forms of the compound that are associated with a solvent or water (also referred to as “hydrate”), usually by a solvolysis reaction. This physical association includes hydrogen bonding.
  • solvents include water, ethanol, acetic acid and the like.
  • the compounds of the invention may be prepared e.g. in crystalline form and may be solvated or hydrated.
  • Suitable solvates include pharmaceutically acceptable solvates, such as hydrates, and further include both stoichiometric solvates and non-stoichiometric solvates. In certain instances the solvate will be capable of isolation, for example when one or more solvent molecules are incorporated in the crystal lattice of the crystalline solid.
  • “Solvate” encompasses both solution-phase and isolable solvates.
  • Representative solvates include hydrates, ethanolates and methanolates.
  • Tautomers refer to compounds that are interchangeable forms of a particular compound structure, and that vary in the displacement of hydrogen atoms and electrons. Thus, two structures may be in equilibrium through the movement of ⁇ electrons and an atom (usually H). For example, enols and ketones are tautomers because they are rapidly interconverted by treatment with either acid or base. Another example of tautomerism is the aci- and nitro-forms of phenylnitromethane, that are likewise formed by treatment with acid or base.
  • Tautomeric forms may be relevant to the attainment of the optimal chemical reactivity and biological activity of a compound of interest.
  • stereoisomers that are not mirror images of one another are termed “diastereomers” and those that are non-superimposable mirror images of each other are termed “enantiomers”.
  • enantiomers When a compound has an asymmetric center, for example, it is bonded to four different groups, a pair of enantiomers is possible.
  • An enantiomer can be characterized by the absolute configuration of its asymmetric center and is described by the R- and S-sequencing rules of Cahn and Prelog, or by the manner in which the molecule rotates the plane of polarized light and designated as dextrorotatory or levorotatory (i.e., as (+) or ( ⁇ )-isomers respectively).
  • a chiral compound can exist as either individual enantiomer or as a mixture thereof. A mixture containing equal proportions of the enantiomers is called a “racemic mixture”.
  • Prodrugs refers to compounds, including derivatives of the compounds of the invention, which have cleavable groups and become by solvolysis or under physiological conditions the compounds of the invention which are pharmaceutically active in vivo. Such examples include, but are not limited to, choline ester derivatives and the like, N-alkylmorpholine esters and the like. Other derivatives of the compounds of this invention have activity in both their acid and acid derivative forms, but in the acid sensitive form often offers advantages of solubility, tissue compatibility, or delayed release in the mammalian organism (see, Bundgard, H., Design of Prodrugs, pp. 7-9, 21-24, Elsevier, Amsterdam 1985).
  • Prodrugs include acid derivatives well know to practitioners of the art, such as, for example, esters prepared by reaction of the parent acid with a suitable alcohol, or amides prepared by reaction of the parent acid compound with a substituted or unsubstituted amine, or acid anhydrides, or mixed anhydrides. Simple aliphatic or aromatic esters, amides and anhydrides derived from acidic groups pendant on the compounds of this invention are particular prodrugs. In some cases it is desirable to prepare double ester type prodrugs such as (acyloxy)alkyl esters or ((alkoxycarbonyl)oxy)alkylesters.
  • C 1 to C 8 alkyl, C 2 -C 8 alkenyl, C 2 -C 8 alkynyl, aryl, C 7 -C 12 substituted aryl, and C 7 -C 12 arylalkyl esters of the compounds of the invention are particularly the C 1 to C 8 alkyl, C 2 -C 8 alkenyl, C 2 -C 8 alkynyl, aryl, C 7 -C 12 substituted aryl, and C 7 -C 12 arylalkyl esters of the compounds of the invention.
  • a “subject” to which administration is contemplated includes, but is not limited to, humans (i.e., a male or female of any age group, e.g., a pediatric subject (e.g, infant, child, adolescent) or adult subject (e.g., young adult, middle-aged adult, or senior adult)) and/or other non-human animals, for example, mammals (e.g., primates (e.g., cynomolgus monkeys, rhesus monkeys); commercially relevant mammals such as cattle, pigs, horses, sheep, goats, cats, and/or dogs) and birds (e.g., commercially relevant birds such as chickens, ducks, geese, and/or turkeys).
  • the animal is a mammal.
  • the animal may be a male or female and at any stage of development.
  • a non-human animal may be a transgenic animal, such as a transgenic mouse or transgenic pig.
  • tissue sample refers to any sample including tissue samples (such as tissue sections and needle biopsies of a tissue); cell samples (e.g., cytological smears (such as Pap or blood smears) or samples of cells obtained by microdissection); samples of whole organisms (such as samples of yeasts or bacteria); or cell fractions, fragments or organelles (such as obtained by lysing cells and separating the components thereof by centrifugation or otherwise).
  • tissue samples such as tissue sections and needle biopsies of a tissue
  • cell samples e.g., cytological smears (such as Pap or blood smears) or samples of cells obtained by microdissection) or samples of cells obtained by microdissection
  • samples of whole organisms such as samples of yeasts or bacteria
  • cell fractions, fragments or organelles such as obtained by lysing cells and separating the components thereof by centrifugation or otherwise.
  • biological samples include blood, serum, urine, semen, fecal matter, cerebrospinal fluid, interstitial fluid, mucus, tears, sweat, pus, biopsied tissue (e.g., obtained by a surgical biopsy or needle biopsy), nipple aspirates, milk, vaginal fluid, saliva, swabs (such as buccal swabs), or any material containing biomolecules that is derived from a first biological sample.
  • Biological samples also include those biological samples that are transgenic, such as transgenic oocyte, sperm cell, blastocyst, embryo, fetus, donor cell, or cell nucleus.
  • Treatment contemplate an action that occurs while a subject is suffering from a condition and that reduces the severity of the condition or retards or slows the progression of the condition (“therapeutic treatment”), and also contemplates an action that occurs before a subject begins to suffer from the condition and that inhibits or reduces the severity of the condition (“prophylactic treatment”).
  • condition As used herein, “condition,” “disease,” and “disorder” are used interchangeably.
  • an “effective amount” of a compound of the present invention refers to an amount sufficient to elicit the desired biological response, i.e., treating the condition.
  • the effective amount of a compound of the invention may vary depending on such factors as the desired biological endpoint, the pharmacokinetics of the compound, the condition being treated, the mode of administration, and the age and health of the subject.
  • An effective amount encompasses therapeutic and prophylactic treatment.
  • an effective amount of an inventive compound may reduce the tumor burden or stop the growth or spread of a tumor.
  • a “therapeutically effective amount” of a compound of the present invention is an amount sufficient to provide a therapeutic benefit in the treatment of a condition or to delay or minimize one or more symptoms associated with the condition.
  • a therapeutically effective amount of a compound means an amount of therapeutic agent, alone or in combination with other therapies, which provides a therapeutic benefit in the treatment of the condition.
  • the term “therapeutically effective amount” can encompass an amount that improves overall therapy, reduces or avoids symptoms or causes of the condition, or enhances the therapeutic efficacy of another therapeutic agent.
  • a “prophylactically effective amount” of a compound of the present invention is an amount sufficient to prevent a condition, or one or more symptoms associated with the condition or prevent its recurrence.
  • a prophylactically effective amount of a compound means an amount of a therapeutic agent, alone or in combination with other agents, which provides a prophylactic benefit in the prevention of the condition.
  • the term “prophylactically effective amount” can encompass an amount that improves overall prophylaxis or enhances the prophylactic efficacy of another prophylactic agent.
  • FIG. 1 includes the chemical structures of representative JNK inhibitors.
  • FIG. 2 depicts the crystal structure (PDB ID 1T46) of c-Kit (ribbons) complexed with imatinib (sticks) ( FIG. 2A ), and the crystal structure (PDB ID 1XBB) of Syk (ribbons) complexed with imatinib (sticks) ( FIG. 2B ).
  • FIG. 3 shows the chemical structures of JNK inhibitors JNK-IN-5 to 12.
  • FIG. 4 depicts a docking result of JNK-IN-7 (sticks) with JNK3 (ribbons). Potential hydrogen-bonding interactions are indicated with dashed lines.
  • FIG. 5 shows the mass spectra obtained from analysis of untreated ( FIG. 5A ) or JNK-IN-7 treated ( FIG. 5B ) recombinant JNK3 kinase domain, and the HCD MS/MS spectrum of the peptide LMDANLC*QVIQME (JNK residues 148-160; C* indicates a labeled cysteine residue) ( FIG. 5C ). Identification of ions of type b and y are indicated with lines above and below the sequence, respectively.
  • FIG. 6 depicts the crystal structure of JNK3 residues 39-402 modified at Cys-154 by JNK-IN-7.
  • the covalent inhibitors and the key residues of JNK3 that are involved in hydrophobic and hydrogen bonding interactions with the covalent inhibitors are labeled and are shown in stick models.
  • the hydrogen bonds between the kinase “hinge” residue Met-149 and the aminopyrimidine-motif of the covalent inhibitors are represented as dotted lines.
  • FIG. 7 is a 2Fo-Fc electron density map corresponding to the covalent inhibitor JNK-IN-7 (sticks). The map is contoured at 1 ⁇ and shows unambiguous electron densities of JNK-IN-7.
  • FIG. 8 shows the kinetics of labeling of JNK in JNK-IN-5, an irreversible JNK inhibitor, compared with JNK-IN-6, a reversible inhibitor.
  • A375 cells were incubated with inhibitors for the indicated amount of time after which cell lysates were prepared and labeled with ATP-biotin. Biotinylated proteins were pulled down with streptavidin beads and material bound to the beads was eluted and separate by SDS-PAGE followed by Western blot analysis for JNK. Complete protection of JNK was achieved following a three-hour incubation with JNK-IN-5 while no protection of JNK labeling was achieved following incubation with JNK-IN-6.
  • FIG. 9 illustrates the cellular kinase selectivity as assessed using the KiNativTM technology. Percent inhibition of kinase labeling by ATP-biotin that results from incubating A375 cells with the inhibitors for 3 hours at a concentration of 1 ⁇ M is indicated (larger numbers indicate stronger binding to the kinase).
  • FIG. 10 shows the sequence alignment of kinases that possess a potentially reactive cysteine (highlighted) that is at least five residues N- and C-terminal to C154 of JNK3.
  • Kinase sequences were retrieved from the human KinBase, and kinome-wide sequence alignment was performed with ClustalX. The gatekeeper amino acid residues are also highlighted.
  • FIG. 11 shows the Kinome ScanTM (DiscoverRx) profiles for the irreversible JNK inhibitors.
  • FIG. 12 shows the enzymatic IC 50 's or dissociation constants (K d ) for the potential additional kinase targets.
  • K d dissociation constants
  • FIG. 13 shows the biochemical IC 50 's for additional kinase targets selected based upon the result of screening a panel of 105 kinases at a concentration of 1 ⁇ M (Dundee Kinase panel).
  • FIG. 14 illustrates the evaluation of the cellular selectivity for the JNK inhibitors as monitored through inhibition of phosphorylation of key nodes on multiple signal transduction pathways.
  • A375 cells were stimulated with anisomycin ( FIGS. 14A , C-F), IGF-1 ( FIG. 14B ), IL-6 ( FIG. 14G ), and TNF- ⁇ ( FIG. 14H ) for sixty minutes.
  • the output of multiple signaling pathways was measured using high throughput microscopy at multiple concentrations of four JNK inhibitors and a control compound specific to each pathway DMSO ( FIG. 14A ), MK2206 (allosteric Akt inhibitor, Haoyuan Chemexpress Co., Limited. Hirai, et al., 2010) ( FIG.
  • FIGS. 14B PD0325901 (allosteric Mek inhibitor, Haoyuan Chemexpress Co., Limited. Barrett, et al., 2008)
  • FIGS. 14C-D SB239063 (ATP-competitive p38 inhibitor, Haoyuan Chemexpress Co., Limited. Underwood et al., 2000)
  • FIGS. 14E-F KIN001-040 (ATP-competitive JAK1,2,3 inhibitor, Haoyuan Chemexpress Co., Limited. Thompson et al., 2002)
  • FIG. 14G KIN001-208 (IKK inhibitor VIII, Haoyuan Chemexpress Co., Limited., Murata, et al., 2004)
  • FIG. 14H KIN001-208 (IKK inhibitor VIII, Haoyuan Chemexpress Co., Limited., Murata, et al., 2004)
  • FIG. 15 shows results of a Western blot analysis of inhibition of JNK, c-Jun, MSK1, and p38 for JNK-IN-7, 8, and 11 following anisomycin stimulation of HEK293-IL1R cells.
  • FIG. 16 depicts Western blot results. Inhibition of phosphorylation of c-Jun is not recovered following “washout” of JNK-IN-8.
  • HEK293-ILR1 cells were treated with JNK-IN-8 for three hours, followed by extensive washout of inhibitor and stimulated with anisomycin for 1 h after the indicated hours ( FIG. 16A ).
  • Cell lysates were prepared, resolved by SDS-PAGE, and p-c-Jun (Ser63) and p-JNK were monitored by Western blot.
  • FIG. 16B shows the inhibition of anisomycin-stimulated c-Jun phosphorylation with varying concentrations and incubation times of JNK-IN-8 in HEK293-ILR1 cells.
  • FIG. 17 shows curves for the determination of K m for ATF2 for JNK WT and JNK Cys116Ser.
  • FIG. 18 shows that mutation of the conserved Cys116 to Ser increases the IC 50 for inhibition of JNK2 by over 100-fold for JNK-IN-7 and JNK-IN-8 but only by approximately 10-fold for JNK-IN-11.
  • the present invention provides compounds that inhibit a kinase, and pharmaceutical compositions thereof, for the prevention and treatment of a disease of a subject.
  • the compounds inhibit c-Jun-N-terminal kinase (JNK).
  • the compounds irreversibly inhibit JNK.
  • the present invention further provides methods of using the compounds described herein, e.g., as biological probes to study the inhibition of JNK activity, and as therapeutics, e.g., in the prevention and treatment of diseases associated with JNK activity.
  • the diseases include, but are not limited to, proliferative diseases (e.g., cancer and benign neoplasms), neurodegenerative diseases, metabolic disorders, inflammatory diseases, and cardiovascular diseases.
  • Ring A is a carbocyclic, heterocyclic, heteroaryl, or aryl ring;
  • each instance of R A is independently selected from the group consisting of hydrogen, halogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —OR A1 , —N(R A1 ) 2 , and —SR A1 , wherein each occurrence of R A1 is independently selected from the group consisting of hydrogen, acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, a sulfur protecting group when attached to a sulfur atom, or two R A1 groups are joined to form an
  • n 0, 1, 2, 3, or 4;
  • Ring B is a group of the formula:
  • R B1 is selected from the group consisting of hydrogen, halogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —OR B1a , —N(R B1a ) 2 , and —SR B1a , wherein each occurrence of R B1a is independently selected from the group consisting of hydrogen, acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, a sulfur protecting group when attached to a sulfur atom, or two R B1a groups are joined to
  • W B is N or CR B2 , wherein R B2 is selected from the group consisting of hydrogen, halogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —OR B2a , —N(R B2a ) 2 , and —SR B2a , wherein each occurrence of R B2a is independently selected from the group consisting of hydrogen, acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, a sulfur protecting group when attached to a sulfur
  • R B1 and R B2 are joined to form an optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted heteroaryl, or optionally substituted aryl ring;
  • L 1 is a bond directly attaching Ring A to Ring B, or L 1 is ⁇ C(R L1a )—, —O—, —S—, —NR L1b —, —NR L1b C( ⁇ O)—, —C( ⁇ O)NR L1b —, —SC( ⁇ O)—, —C( ⁇ O)S—, —OC( ⁇ O)—, —C( ⁇ O)O—, —NR L1b C( ⁇ S)—, —C( ⁇ S)NR L1b —, trans-CH ⁇ CH—, cis-CH ⁇ CH—, —S( ⁇ O) 2 O—, —OS( ⁇ O) 2 —, —S( ⁇ O) 2 NR L1b —, —NR L1b S( ⁇ O) 2 —, or an optionally substituted C 1-4 hydrocarbon chain, optionally wherein one methylene unit of the hydrocarbon chain is replaced with ⁇ C(R L1a )—,
  • X is an optionally substituted C 1-4 hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain is replaced with —O—, —S—, or —NR X —, wherein R X is hydrogen, C 1-6 alkyl, or a nitrogen protecting group;
  • L 2 is a bond, —O—, —S—, —NR L2a —, —NR L2a C( ⁇ O)—, —C( ⁇ O)NR L2a —, —SC( ⁇ O)—, —C( ⁇ O)S—, —OC( ⁇ O)—, —C( ⁇ O)O—, —NR L2a C( ⁇ S)—, —C( ⁇ S)NR L2a —, trans-CR L2b ⁇ CR L2b —, cis-CR L2b ⁇ CR L2b —, —C ⁇ C—, —OC(R L2b ) 2 —, —C(R L2b ) 2 O—, —NR L2a C(R L2b ) 2 —, —C(R L2b ) 2 NR L2a —, —SC(R L2b ) 2 —, —C(R L2b ) 2 S—, —S(
  • each instance of R C is independently selected from the group consisting of hydrogen, halogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —OR C1 , —N(R C1 ) 2 , and —SR C1 , wherein each occurrence of R C1 is independently selected from the group consisting of hydrogen, acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, a sulfur protecting group when attached to a sulfur atom, or two R C1 groups are joined to form an
  • n 0, 1, 2, 3, or 4;
  • each instance of R D is independently selected from the group consisting of hydrogen, halogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —OR D1 , —N(R D1 ) 2 , and —SR D1 , wherein each occurrence of R D1 is independently selected from the group consisting of hydrogen, acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, a sulfur protecting group when attached to a sulfur atom, or two R D1 groups are joined to form an
  • p 0, 1, 2, 3, or 4;
  • R E is a group of the formula:
  • L 3 is a bond, —O—, —S—, —NR L3a —, —NR L3a C( ⁇ O)—, —C( ⁇ O)NR L3a —, —SC( ⁇ O)—, —C( ⁇ O)S—, —OC( ⁇ O)—, —C( ⁇ O)O—, —NR L3a C( ⁇ S)—, —C( ⁇ S)NR L3a —, trans-CR L3b ⁇ CR L3b —, cis-CR L3b ⁇ CR L3b —, —C ⁇ C—, —OC(R L3b ) 2 —, —C(R L3b ) 2 O—, —NR L3a C(R L3b ) 2 —, —C(R L3b ) 2 NR L3a —, —SC(R L3b ) 2 —, —C(R L3b ) 2 S—, —S(
  • L 4 is a bond or an optionally substituted C 1-4 hydrocarbon chain
  • R E1 is selected from the group consisting of hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CH 2 OR E1a , —CH 2 N(R E1a ) 2 , —CH 2 SR E1a , —OR E1a , —N(R E1a ) 2 , and —SR E1a , wherein each occurrence of R E1a is independently selected from the group consisting of hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, and optionally substituted heteroaryl, or two R E1a groups are joined to form an optionally substituted heterocyclic ring;
  • R E2 is selected from the group consisting of hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CH 2 OR E2a , —CH 2 N(R E2a ) 2 , —CH 2 SR E2a , —OR E2a , —N(R E2a ) 2 , and —SR E2a , wherein each occurrence of R E2a is independently selected from the group consisting of hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, and optionally substituted heteroaryl, or two R E2a groups are joined to form an optionally substituted heterocyclic ring;
  • R E3 is selected from the group consisting of hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CH 2 OR E3a , —CH 2 N(R E3a ) 2 , —CH 2 SR E3a , —OR E3a , —N(R E3a ) 2 , and —SR E3a , wherein each occurrence of R E3a is independently selected from the group consisting of hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, and optionally substituted heteroaryl, or two R E3a groups are joined to form an optionally substituted heterocyclic ring;
  • R E1 and R E3 or R E2 and R E3 or R E1 and R E2 are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring;
  • R E4 is a leaving group
  • Y is O, S, or NR E5 , wherein R E5 is hydrogen, C 1-6 alkyl, or a nitrogen protecting group;
  • a is 1 or 2;
  • z 0, 1, 2, 3, 4, 5, or 6.
  • Ring A may be substituted with one or more substitutents R A .
  • Ring A is a carbocyclic ring.
  • Ring A is a monocyclic carbocyclic ring.
  • Ring A is a bicyclic carbocyclic ring.
  • Ring A is a tricyclic carbocyclic ring.
  • Ring A is a substituted carbocyclic ring.
  • Ring A is an unsubstituted carbocyclic ring.
  • Ring A is a saturated carbocyclic ring. In certain embodiments, Ring A is an unsaturated carbocyclic ring. In certain embodiments, Ring A is a carbocyclic ring fused with one or more carbocyclic, heterocyclic, aryl, or heteroaryl groups wherein the point of attachment is on the carbocyclic ring.
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is a heterocyclic ring. In certain embodiments, Ring A is a monocyclic heterocyclic ring. In certain embodiments, Ring A is a bicyclic heterocyclic ring. In certain embodiments, Ring A is a tricyclic heterocyclic ring. In certain embodiments, Ring A is a substituted heterocyclic ring. In certain embodiments, Ring A is an unsubstituted heterocyclic ring. In certain embodiments, Ring A is a saturated heterocyclic ring. In certain embodiments, Ring A is an unsaturated heterocyclic ring. In certain embodiments, Ring A is a heterocyclic ring fused with one or more carbocyclic, heterocyclic, aryl, or heteroaryl groups wherein the point of attachment is on the heterocyclic ring.
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is an aryl ring. In certain embodiments, Ring A is a monocyclic aryl ring. In certain embodiments, Ring A is a bicyclic aryl ring. In certain embodiments, Ring A is a tricyclic aryl ring. In certain embodiments, Ring A is a substituted aryl ring. In certain embodiments, Ring A is an unsubstituted aryl ring. In certain embodiments, Ring A is substituted phenyl. In certain embodiments, Ring A is unsubstituted phenyl.
  • Ring A is an aryl ring fused with one or more carbocyclic, heterocyclic, aryl, or heteroaryl groups wherein the point of attachment is on the aryl ring. In certain embodiments, Ring A is substituted naphthyl. In certain embodiments, Ring A is unsubstituted naphthyl.
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A of Formula (I) may also be an optionally substituted heteroaryl ring.
  • Ring A is a substituted heteroaryl ring.
  • Ring A is an unsubstituted heteroaryl ring.
  • Ring A is a monocyclic heteroaryl ring.
  • Ring A is a 5-membered monocyclic heteroaryl ring.
  • Ring A is a 5-membered monocyclic heteroaryl ring with one heteroatom selected from the group consisting of S, N, and O.
  • Ring A is a 5-membered monocyclic heteroaryl ring with two heteroatoms selected from the group consisting of S, N, and O.
  • Ring A is a 5-membered monocyclic heteroaryl ring with three heteroatoms selected from the group consisting of S, N, and O.
  • Ring A is substituted pyrrolyl.
  • Ring A is unsubstituted pyrrolyl.
  • Ring A is substituted furanyl.
  • Ring A is unsubstituted furanyl.
  • Ring A is substituted thienyl.
  • Ring A is unsubstituted thienyl.
  • Ring A is substituted pyrazolyl.
  • Ring A is unsubstituted pyrazolyl.
  • Ring A is substituted imidazolyl. In certain embodiments, Ring A is unsubstituted imidazolyl. In certain embodiments, Ring A is substituted oxazolyl. In certain embodiments, Ring A is unsubstituted oxazolyl. In certain embodiments, Ring A is substituted isoxazolyl. In certain embodiments, Ring A is unsubstituted isoxazolyl. In certain embodiments, Ring A is substituted thiazolyl. In certain embodiments, Ring A is unsubstituted thiazolyl. In certain embodiments, Ring A is substituted isothiazolyl. In certain embodiments, Ring A is unsubstituted isothiazolyl.
  • Ring A is substituted triazolyl. In certain embodiments, Ring A is unsubstituted triazolyl. In certain embodiments, Ring A is substituted oxadiazolyl. In certain embodiments, Ring A is unsubstituted oxadiazolyl. In certain embodiments, Ring A is substituted thiadiazolyl. In certain embodiments, Ring A is unsubstituted thiadiazolyl. In certain embodiments, Ring A is a 6-membered monocyclic heteroaryl ring. In certain embodiments, Ring A is a 6-membered monocyclic heteroaryl ring with one heteroatom selected from the group consisting of S, N, and O.
  • Ring A is a 6-membered monocyclic heteroaryl ring with two heteroatoms selected from the group consisting of S, N, and O. In certain embodiments, Ring A is a 6-membered monocyclic heteroaryl ring with three heteroatoms selected from the group consisting of S, N, and O. In certain embodiments, Ring A is substituted pyridyl. In certain embodiments, Ring A is unsubstituted pyridyl. In certain embodiments, Ring A is substituted pyridazinyl. In certain embodiments, Ring A is unsubstituted pyridazinyl. In certain embodiments, Ring A is substituted pyrimidinyl.
  • Ring A is unsubstituted pyrimidinyl. In certain embodiments, Ring A is substituted pyrazinyl. In certain embodiments, Ring A is unsubstituted pyrazinyl. In certain embodiments, Ring A is substituted triazinyl. In certain embodiments, Ring A is unsubstituted triazinyl.
  • Ring A is an optionally substituted heteroaryl ring fused with one or more optionally substituted carbocyclic, optionally substituted heterocyclic, optionally substituted aryl, or optionally substituted heteroaryl groups wherein the point of attachment is on any one of the heteroaryl ring, or carbocyclic, heterocyclic, aryl, or heteroaryl groups, as valency permits.
  • Ring A is a bicyclic heteroaryl ring.
  • Ring A is an optionally substituted heteroaryl ring fused with an optionally substituted phenyl ring.
  • Ring A is substituted indolyl.
  • Ring A is unsubstituted indolyl.
  • Ring A is substituted isoindolyl. In certain embodiments, Ring A is unsubstituted isoindolyl. In certain embodiments, Ring A is substituted indazolyl. In certain embodiments, Ring A is unsubstituted indazolyl. In certain embodiments, Ring A is substituted benzothienyl. In certain embodiments, Ring A is unsubstituted benzothienyl. In certain embodiments, Ring A is substituted isobenzothienyl. In certain embodiments, Ring A is unsubstituted isobenzothienyl. In certain embodiments, Ring A is substituted benzofuranyl. In certain embodiments, Ring A is unsubstituted benzofuranyl.
  • Ring A is substituted benzoisofuranyl. In certain embodiments, Ring A is unsubstituted benzoisofuranyl. In certain embodiments, Ring A is substituted benzimidazolyl. In certain embodiments, Ring A is unsubstituted benzimidazolyl. In certain embodiments, Ring A is substituted benzoxazolyl. In certain embodiments, Ring A is unsubstituted benzoxazolyl. In certain embodiments, Ring A is substituted benzisoxazolyl. In certain embodiments, Ring A is unsubstituted benzisoxazolyl. In certain embodiments, Ring A is substituted benzothiazolyl.
  • Ring A is unsubstituted benzothiazolyl. In certain embodiments, Ring A is substituted benzisothiazolyl. In certain embodiments, Ring A is unsubstituted benzisothiazolyl. In certain embodiments, Ring A is substituted benzotriazolyl. In certain embodiments, Ring A is unsubstituted benzotriazolyl. In certain embodiments, Ring A is substituted benzoxadiazolyl. In certain embodiments, Ring A is unsubstituted benzoxadiazolyl. In certain embodiments, Ring A is substituted quinolinyl. In certain embodiments, Ring A is unsubstituted quinolinyl.
  • Ring A is substituted isoquinolinyl. In certain embodiments, Ring A is unsubstituted isoquinolinyl. In certain embodiments, Ring A is substituted cinnolinyl. In certain embodiments, Ring A is unsubstituted cinnolinyl. In certain embodiments, Ring A is substituted quinoxalinyl. In certain embodiments, Ring A is unsubstituted quinoxalinyl. In certain embodiments, Ring A is substituted phthalazinyl. In certain embodiments, Ring A is unsubstituted phthalazinyl. In certain embodiments, Ring A is substituted quinazolinyl. In certain embodiments, Ring A is unsubstituted quinazolinyl. In certain embodiments, Ring A is a tricyclic heteroaryl ring.
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • At least one R A is H. In certain embodiments, at least one R A is halogen. In certain embodiments, at least one R A is F. In certain embodiments, at least one R A is Cl. In certain embodiments, at least one R A is Br. In certain embodiments, at least one R A is I (iodine). In certain embodiments, at least one R A is acyl. In certain embodiments, at least one R A is acetyl. In certain embodiments, at least one R A is substituted alkyl. In certain embodiments, at least one R A is unsubstituted alkyl. In certain embodiments, at least one R A is C 1-6 alkyl. In certain embodiments, at least one R A is methyl.
  • At least one R A is ethyl. In certain embodiments, at least one R A is propyl. In certain embodiments, at least one R A is butyl. In certain embodiments, at least one R A is substituted alkenyl. In certain embodiments, at least one R A is unsubstituted alkenyl. In certain embodiments, at least one R A is substituted alkynyl. In certain embodiments, at least one R A is unsubstituted alkynyl. In certain embodiments, at least one R A is substituted carbocyclyl. In certain embodiments, at least one R A is unsubstituted carbocyclyl. In certain embodiments, at least one R A is substituted heterocyclyl.
  • At least one R A is unsubstituted heterocyclyl. In certain embodiments, at least one R A is substituted aryl. In certain embodiments, at least one R A is unsubstituted aryl. In certain embodiments, at least one R A is substituted phenyl. In certain embodiments, at least one R A is unsubstituted phenyl. In certain embodiments, at least one R A is substituted heteroaryl. In certain embodiments, at least one R A is unsubstituted heteroaryl. In certain embodiments, at least one R A is substituted pyridyl. In certain embodiments, at least one R A is unsubstituted pyridyl. In certain embodiments, at least one R A is —OR A1 . In certain embodiments, at least one R A is —N(R A1 ) 2 . In certain embodiments, at least one R A is —SR A1 .
  • R A when R A is —OR A1 , —N(R A1 ) 2 , or —SR A1 , at least one R A1 is H. In certain embodiments, at least one R A1 is acyl. In certain embodiments, at least one R A1 is acetyl. In certain embodiments, at least one R A1 is substituted alkyl. In certain embodiments, at least one R A1 is unsubstituted alkyl. In certain embodiments, at least one R A1 is C 1-6 alkyl. In certain embodiments, at least one R A1 is methyl. In certain embodiments, at least one R A1 is ethyl. In certain embodiments, at least one R A1 is propyl.
  • At least one R A1 is butyl. In certain embodiments, at least one R A1 is substituted alkenyl. In certain embodiments, at least one R A1 is unsubstituted alkenyl. In certain embodiments, at least one R A1 is substituted alkynyl. In certain embodiments, at least one R A1 is unsubstituted alkynyl. In certain embodiments, at least one R A1 is substituted carbocyclyl. In certain embodiments, at least one R A1 is unsubstituted carbocyclyl. In certain embodiments, at least one R A1 is substituted heterocyclyl. In certain embodiments, at least one R A1 is unsubstituted heterocyclyl.
  • At least one R A1 is substituted aryl. In certain embodiments, at least one R A1 is unsubstituted aryl. In certain embodiments, at least one R A1 is substituted phenyl. In certain embodiments, at least one R A1 is unsubstituted phenyl. In certain embodiments, at least one R A1 is substituted heteroaryl. In certain embodiments, at least one R A1 is unsubstituted heteroaryl. In certain embodiments, at least one R A1 is substituted pyridyl. In certain embodiments, at least one R A1 is unsubstituted pyridyl.
  • At least one R A1 is a nitrogen protecting group when attached to a nitrogen atom. In certain embodiments, at least one R A1 is an oxygen protecting group when attached to an oxygen atom. In certain embodiments, at least one R A1 is a sulfur protecting group when attached to a sulfur atom. In certain embodiments, two R A1 groups are joined to form a substituted heterocyclic ring. In certain embodiments, two R A1 groups are joined to form an unsubstituted heterocyclic ring.
  • Ring A may be unsubstituted or substituted with one or more R A . In certain embodiments, Ring A is unsubstituted, and thus m is 0. In certain embodiments, m is 1. In certain embodiments, m is 2. In certain embodiments, m is 3. In certain embodiments, m is 4.
  • Compounds of Formula (I) include a substituted or unsubstituted heteroaryl ring as Ring B.
  • Ring B may be substituted with one substituent R B1 or two substituents R B1 and R B2 .
  • Ring B is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Ring B is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • R B1 is H. In certain embodiments, R B1 is halogen. In certain embodiments, R B1 is F. In certain embodiments, R B1 is Cl. In certain embodiments, R B1 is Br. In certain embodiments, R B1 is I (iodine). In certain embodiments, R B1 is acyl. In certain embodiments, R B1 is acetyl. In certain embodiments, R B1 is substituted alkyl. In certain embodiments, R B1 is unsubstituted alkyl. In certain embodiments, R B1 is C 1-6 alkyl. In certain embodiments, R B1 is methyl. In certain embodiments, R B1 is ethyl. In certain embodiments, R B1 is propyl.
  • R B1 is butyl. In certain embodiments, R B1 is substituted alkenyl. In certain embodiments, R B1 is unsubstituted alkenyl. In certain embodiments, R B1 is substituted alkynyl. In certain embodiments, R B1 is unsubstituted alkynyl. In certain embodiments, R B1 is substituted carbocyclyl. In certain embodiments, R B1 is unsubstituted carbocyclyl. In certain embodiments, R B1 is substituted heterocyclyl. In certain embodiments, R B1 is unsubstituted heterocyclyl. In certain embodiments, R B1 is substituted aryl.
  • R B1 is unsubstituted aryl. In certain embodiments, R B1 is substituted phenyl. In certain embodiments, R B1 is unsubstituted phenyl. In certain embodiments, R B1 is substituted heteroaryl. In certain embodiments, R B1 is unsubstituted heteroaryl. In certain embodiments, R B1 is substituted pyridyl. In certain embodiments, R B1 is unsubstituted pyridyl. In certain embodiments, R B1 is —OR B1a . In certain embodiments, R B1 is —N(R B1a ) 2 . In certain embodiments, R B1 is —SR B1a .
  • At least one R B1a is H. In certain embodiments, at least one R B1a is acyl. In certain embodiments, at least one R B1a is acetyl. In certain embodiments, at least one R B1a is substituted alkyl. In certain embodiments, at least one R B1a is unsubstituted alkyl. In certain embodiments, at least one R B1a is C 1-6 alkyl. In certain embodiments, at least one R B1a is methyl. In certain embodiments, at least one R B1a is ethyl. In certain embodiments, at least one R B1a is propyl. In certain embodiments, at least one R B1a is butyl.
  • At least one R B1a is substituted alkenyl. In certain embodiments, at least one R B1a is unsubstituted alkenyl. In certain embodiments, at least one R B1a is substituted alkynyl. In certain embodiments, at least one R B1a is unsubstituted alkynyl. In certain embodiments, at least one R B1a is substituted carbocyclyl. In certain embodiments, at least one R B1a is unsubstituted carbocyclyl. In certain embodiments, at least one R B1a is substituted heterocyclyl. In certain embodiments, at least one R B1a is unsubstituted heterocyclyl.
  • At least one R B1a is substituted aryl. In certain embodiments, at least one R B1a is unsubstituted aryl. In certain embodiments, at least one R B1a is substituted phenyl. In certain embodiments, at least one R B1a is unsubstituted phenyl. In certain embodiments, at least one R B1a is substituted heteroaryl. In certain embodiments, at least one R B1a is unsubstituted heteroaryl. In certain embodiments, at least one R B1a is substituted pyridyl. In certain embodiments, at least one R B1a is unsubstituted pyridyl.
  • At least one R B1a is a nitrogen protecting group when attached to a nitrogen atom. In certain embodiments, at least one R B1a is an oxygen protecting group when attached to an oxygen atom. In certain embodiments, at least one R B1a is a sulfur protecting group when attached to a sulfur atom. In certain embodiments, two R B1a groups are joined to form a substituted heterocyclic ring. In certain embodiments, two R B1a groups are joined to form an unsubstituted heterocyclic ring.
  • R B2 is H. In certain embodiments, R B2 is halogen. In certain embodiments, R B2 is F. In certain embodiments, R B2 is Cl. In certain embodiments, R B2 is Br. In certain embodiments, R B2 is I (iodine). In certain embodiments, R B2 is acyl. In certain embodiments, R B2 is acetyl. In certain embodiments, R B2 is substituted alkyl. In certain embodiments, R B2 is unsubstituted alkyl. In certain embodiments, R B2 is C 1-6 alkyl. In certain embodiments, R B2 is methyl. In certain embodiments, R B2 is ethyl. In certain embodiments, R B2 is propyl.
  • R B2 is butyl. In certain embodiments, R B2 is substituted alkenyl. In certain embodiments, R B2 is unsubstituted alkenyl. In certain embodiments, R B2 is substituted alkynyl. In certain embodiments, R B2 is unsubstituted alkynyl. In certain embodiments, R B2 is substituted carbocyclyl. In certain embodiments, R B2 is unsubstituted carbocyclyl. In certain embodiments, R B2 is substituted heterocyclyl. In certain embodiments, R B2 is unsubstituted heterocyclyl. In certain embodiments, R B2 is substituted aryl.
  • R B2 is unsubstituted aryl. In certain embodiments, R B2 is substituted phenyl. In certain embodiments, R B2 is unsubstituted phenyl. In certain embodiments, R B2 is substituted heteroaryl. In certain embodiments, R B2 is unsubstituted heteroaryl. In certain embodiments, R B2 is substituted pyridyl. In certain embodiments, R B2 is unsubstituted pyridyl. In certain embodiments, R B2 is —OR B2a . In certain embodiments, R B2 is —N(R B2a ) 2 . In certain embodiments, R B2 is —SR B2a .
  • At least one R B2a is H. In certain embodiments, at least one R B2a is acyl. In certain embodiments, at least one R B2a is acetyl. In certain embodiments, at least one R B2a is substituted alkyl. In certain embodiments, at least one R B2a is unsubstituted alkyl. In certain embodiments, at least one R B2a is C 1-6 alkyl. In certain embodiments, at least one R B2a is methyl. In certain embodiments, at least one R B2a is ethyl. In certain embodiments, at least one R B2a is propyl. In certain embodiments, at least one R B2a is butyl.
  • At least one R B2a is substituted alkenyl. In certain embodiments, at least one R B2a is unsubstituted alkenyl. In certain embodiments, at least one R B2a is substituted alkynyl. In certain embodiments, at least one R B2a is unsubstituted alkynyl. In certain embodiments, at least one R B2a is substituted carbocyclyl. In certain embodiments, at least one R B2a is unsubstituted carbocyclyl. In certain embodiments, at least one R B2a is substituted heterocyclyl. In certain embodiments, at least one R B2a is unsubstituted heterocyclyl.
  • At least one R B2a is substituted aryl. In certain embodiments, at least one R B2a is unsubstituted aryl. In certain embodiments, at least one R B2a is substituted phenyl. In certain embodiments, at least one R B2a is unsubstituted phenyl. In certain embodiments, at least one R B2a is substituted heteroaryl. In certain embodiments, at least one R B2a is unsubstituted heteroaryl. In certain embodiments, at least one R B2a is substituted pyridyl. In certain embodiments, at least one R B2a is unsubstituted pyridyl.
  • At least one R B2a is a nitrogen protecting group when attached to a nitrogen atom. In certain embodiments, at least one R B2a is an oxygen protecting group when attached to an oxygen atom. In certain embodiments, at least one R B2a is a sulfur protecting group when attached to a sulfur atom. In certain embodiments, two R B2a groups are joined to form a substituted heterocyclic ring. In certain embodiments, two R B2a groups are joined to form an unsubstituted heterocyclic ring.
  • R B1 and R B2 are joined to form a substituted carbocyclic ring. In certain embodiments, R B1 and R B2 are joined to form an unsubstituted carbocyclic ring. In certain embodiments, R B1 and R B2 are joined to form a substituted heterocyclic ring. In certain embodiments, R B1 and R B2 are joined to form an unsubstituted heterocyclic ring. In certain embodiments, R B1 and R B2 are joined to form a substituted heteroaryl ring. In certain embodiments, R B1 and R B2 are joined to form an unsubstituted heteroaryl ring.
  • R B1 and R B2 are joined to form a substituted pyridyl ring. In certain embodiments, R B1 and R B2 are joined to form an unsubstituted pyridyl ring. In certain embodiments, R B1 and R B2 are joined to form a substituted aryl ring. In certain embodiments, R B1 and R B2 are joined to form an unsubstituted aryl ring. In certain embodiments, R B1 and R B2 are joined to form a substituted phenyl ring. In certain embodiments, R B1 and R B2 are joined to form an unsubstituted phenyl ring.
  • Ring B is a group selected from the group consisting of:
  • R B3 is selected from the group consisting of hydrogen, halogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —OR B3a , —N(R B3a ) 2 , and —SR B3a , wherein each occurrence of R B3a is independently selected from the group consisting of hydrogen, acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, a sulfur protecting group when attached to a sulfur atom, or two R B3a groups are joined to
  • q 0, 1, 2, or 3.
  • R B3 is H. In certain embodiments, R B3 is halogen. In certain embodiments, R B3 is F. In certain embodiments, R B3 is Cl. In certain embodiments, R B3 is Br. In certain embodiments, R B3 is I (iodine). In certain embodiments, R B3 is acyl. In certain embodiments, R B3 is acetyl. In certain embodiments, R B3 is substituted alkyl. In certain embodiments, R B3 is unsubstituted alkyl. In certain embodiments, R B3 is C 1-6 alkyl. In certain embodiments, R B3 is methyl. In certain embodiments, R B3 is ethyl. In certain embodiments, R B3 is propyl.
  • R B3 is butyl. In certain embodiments, R B3 is substituted alkenyl. In certain embodiments, R B3 is unsubstituted alkenyl. In certain embodiments, R B3 is substituted alkynyl. In certain embodiments, R B3 is unsubstituted alkynyl. In certain embodiments, R B3 is substituted carbocyclyl. In certain embodiments, R B3 is unsubstituted carbocyclyl. In certain embodiments, R B3 is substituted heterocyclyl. In certain embodiments, R B3 is unsubstituted heterocyclyl. In certain embodiments, R B3 is substituted aryl.
  • R B3 is unsubstituted aryl. In certain embodiments, R B3 is substituted phenyl. In certain embodiments, R B3 is unsubstituted phenyl. In certain embodiments, R B3 is substituted heteroaryl. In certain embodiments, R B3 is unsubstituted heteroaryl. In certain embodiments, R B3 is substituted pyridyl. In certain embodiments, R B3 is unsubstituted pyridyl. In certain embodiments, R B3 is —OR B3a . In certain embodiments, R B3 is —N(R B3a ) 2 . In certain embodiments, R B3 is —SR B3a .
  • At least one R B3a is H. In certain embodiments, at least one R B3a is acyl. In certain embodiments, at least one R B3a is acetyl. In certain embodiments, at least one R B3a is substituted alkyl. In certain embodiments, at least one R B3a is unsubstituted alkyl. In certain embodiments, at least one R B3a is C 1-6 alkyl. In certain embodiments, at least one R B3a is methyl. In certain embodiments, at least one R B3a is ethyl. In certain embodiments, at least one R B3a is propyl. In certain embodiments, at least one R B3a is butyl.
  • At least one R B3a is substituted alkenyl. In certain embodiments, at least one R B3a is unsubstituted alkenyl. In certain embodiments, at least one R B3a is substituted alkynyl. In certain embodiments, at least one R B3a is unsubstituted alkynyl. In certain embodiments, at least one R B3a is substituted carbocyclyl. In certain embodiments, at least one R B3a is unsubstituted carbocyclyl. In certain embodiments, at least one R B3a is substituted heterocyclyl. In certain embodiments, at least one R B3a is unsubstituted heterocyclyl.
  • At least one R B3a is substituted aryl. In certain embodiments, at least one R B3a is unsubstituted aryl. In certain embodiments, at least one R B3a is substituted phenyl. In certain embodiments, at least one R B3a is unsubstituted phenyl. In certain embodiments, at least one R B3a is substituted heteroaryl. In certain embodiments, at least one R B3a is unsubstituted heteroaryl. In certain embodiments, at least one R B3a is substituted pyridyl. In certain embodiments, at least one R B3a is unsubstituted pyridyl.
  • At least one R B3a is a nitrogen protecting group when attached to a nitrogen atom. In certain embodiments, at least one R B3a is an oxygen protecting group when attached to an oxygen atom. In certain embodiments, at least one R B3a is a sulfur protecting group when attached to a sulfur atom. In certain embodiments, two R B3a groups are joined to form a substituted heterocyclic ring. In certain embodiments, two R B3a groups are joined to form an unsubstituted heterocyclic ring.
  • Ring B may be unsubstituted or substituted with one or more R B3 .
  • Ring B is unsubstituted, and thus q is 0.
  • q is 1.
  • q is 2.
  • q is 3.
  • L 1 is a divalent linker moiety.
  • L 1 may contain 0-4 carbon or hetero atoms in the backbone of L 1 .
  • L 1 may be saturated or unsaturated.
  • L 1 may be substituted or unsubstituted.
  • L 1 is a bond directly attaching Ring A to Ring B.
  • L 1 is a single bond.
  • L 1 is a double bond.
  • L 1 is —O—.
  • L 1 is —S—.
  • L 1 is —NR L1b —.
  • L 1 is —NH—.
  • L 1 is —NR L1b C( ⁇ O)—.
  • L 1 is —NHC( ⁇ O)—. In certain embodiments, L 1 is —C( ⁇ O)NR L1b —. In certain embodiments, L 1 is —C( ⁇ O)NH—. In certain embodiments, L 1 is —SC( ⁇ O)—. In certain embodiments, L 1 is —C( ⁇ O)S—. In certain embodiments, L 1 is —OC( ⁇ O)—In certain embodiments, L 1 is —C( ⁇ O)O—. In certain embodiments, L 1 is —NR L1b C( ⁇ S)—. In certain embodiments, L 1 is —NHC( ⁇ S)—. In certain embodiments, L 1 is —C( ⁇ S)NR L1b —.
  • L 1 is —C( ⁇ S)NH—. In certain embodiments, L 1 is trans-CH ⁇ CH—. In certain embodiments, L 1 is cis-CH ⁇ CH—. In certain embodiments, L 1 is —S( ⁇ O) 2 O—. In certain embodiments, L 1 is —OS( ⁇ O) 2 —. In certain embodiments, L 1 is —S( ⁇ O) 2 NR L1b —. In certain embodiments, L 1 is —S( ⁇ O) 2 NH—. In certain embodiments, L 1 is —NR L1b S( ⁇ O) 2 —. In certain embodiments, L 1 is —NHS( ⁇ O) 2 —.
  • L 1 is an unsubstituted C 1-4 hydrocarbon chain. In certain embodiments, L 1 is a substituted C 1-4 hydrocarbon chain. In certain embodiments, L 1 is a substituted or unsubstituted C 1-4 hydrocarbon chain, wherein one methylene unit of the hydrocarbon chain is replaced with ⁇ C(R L1a )—, —O—, —S—, —NR L1b —, —NR L1b C( ⁇ O)—, —C( ⁇ O)NR L1b —, —SC( ⁇ O)—, —C( ⁇ O)S—, —OC( ⁇ O)—, —C( ⁇ O)O—, —NR L1b C( ⁇ S)—, —C( ⁇ S)NR L1b —, trans-CH ⁇ CH—, cis-CH ⁇ CH—, —S( ⁇ O) 2 O—, —OS( ⁇ O) 2 —, —S( ⁇ O) 2 NR L1
  • between L 1 and Ring A is a single bond. In certain embodiments, with respect to Formula (I), is a double bond.
  • X is a divalent linker moiety.
  • X may be an optionally substituted C 1-4 hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain is replaced with —O—, —S—, or —NR X —.
  • X is a C 1 hydrocarbon chain, optionally wherein the carbon unit of the hydrocarbon chain is replaced with —O—, —S—, or —NR X —.
  • X is —O—.
  • X is —S—.
  • X is —NR X —.
  • X is —NH—.
  • X is —C(R X ) 2 —.
  • X is —CH 2 —.
  • R X when X is —NR X — or —C(R X ) 2 —, R X is H.
  • R X is substituted alkyl.
  • R X is unsubstituted alkyl.
  • R X is C 1-6 alkyl.
  • R X is methyl.
  • R X is ethyl.
  • R X is propyl.
  • R X is butyl.
  • R X when X is —NR X —, R X is a nitrogen protecting group.
  • R X is BOC. In certain embodiments, R X is Cbz. In certain embodiments, R X is Fmoc. In certain embodiments, R X is Bn. In certain embodiments, X is a C 2 hydrocarbon chain, optionally wherein one or two carbon units of the hydrocarbon chain is replaced with —O—, —S—, or —NR X —. In certain embodiments, X is a C 3 hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain is replaced with —O—, —S—, or —NR X —. In certain embodiments, X is a C 4 hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain is replaced with —O—, —S—, or —NR X —.
  • L 2 is a divalent linker moiety.
  • L 2 may contain 0-4 carbon or hetero atoms in the backbone of L 2 .
  • L 2 may be saturated or unsaturated.
  • L 2 may be substituted or unsubstituted.
  • L 2 may be branched or unbranched.
  • L 2 is a bond.
  • L 2 is —O—.
  • L 2 is —S—.
  • L 2 is —NR L2a —.
  • L 2 is —NH—.
  • L 2 is —NR L2a C( ⁇ O)—.
  • L 2 is —NHC( ⁇ O)—.
  • L 2 is —C( ⁇ O)NR L2a —. In certain embodiments, L 2 is —C( ⁇ O)NH—. In certain embodiments, L 2 is —SC( ⁇ O)—. In certain embodiments, L 2 is —C( ⁇ O)S—. In certain embodiments, L 2 is —OC( ⁇ O)—. In certain embodiments, L 2 is —C( ⁇ O)O—. In certain embodiments, L 2 is —NR L2a C( ⁇ S)—. In certain embodiments, L 2 is —NHC( ⁇ S)—. In certain embodiments, L 2 is —C( ⁇ S)NR L2a —. In certain embodiments, L 2 is —C( ⁇ S)NH—.
  • L 2 is trans-CR L2b ⁇ CR L2b —. In certain embodiments, L 2 is trans-CH ⁇ CH—. In certain embodiments, L 2 is cis-CR L2b ⁇ CR L2b —. In certain embodiments, L 2 is cis-CH ⁇ CH—. In certain embodiments, L 2 is —C ⁇ C—. In certain embodiments, L 2 is —OC(R L2b ) 2 —. In certain embodiments, L 2 is —OCH 2 —. In certain embodiments, L 2 is —C(R L2b ) 2 —. In certain embodiments, L 2 is —CH 2 O—.
  • L 2 is —NR L2a C(R L2b ) 2 —. In certain embodiments, L 2 is —NR L2a CH 2 —. In certain embodiments, L 2 is —NHCH 2 —. In certain embodiments, L 2 is —C(R L2b ) 2 NR L2a —. In certain embodiments, L 2 is —CH 2 NR L2a —. In certain embodiments, L 2 is —CH 2 NH—. In certain embodiments, L 2 is —SC(R L2b ) 2 —. In certain embodiments, L 2 is —SCH 2 —. In certain embodiments, L 2 is —C(R L2b ) 2 S—.
  • L 2 is —CH 2 S—. In certain embodiments, L 2 is —S( ⁇ O) 2 O—. In certain embodiments, L 2 is —OS( ⁇ O) 2 —. In certain embodiments, L 2 is —S( ⁇ O) 2 NR L2a —. In certain embodiments, L 2 is —S( ⁇ O) 2 NH—. In certain embodiments, L 2 is —NR L2a S( ⁇ O) 2 —. In certain embodiments, L 2 is —NHS( ⁇ O) 2 —. In certain embodiments, L 2 is a substituted C 1-4 hydrocarbon chain. In certain embodiments, L 2 is an unsubstituted C 1-4 hydrocarbon chain.
  • L 2 is a substituted C 2 hydrocarbon chain. In certain embodiments, L 2 is an unsubstituted C 2 hydrocarbon chain. In certain embodiments, L 2 is a substituted C 3 hydrocarbon chain. In certain embodiments, L 2 is an unsubstituted C 3 hydrocarbon chain. In certain embodiments, L 2 is a substituted C 4 hydrocarbon chain. In certain embodiments, L 2 is an unsubstituted C 4 hydrocarbon chain.
  • L 2 is an optionally substituted C 1-4 hydrocarbon chain, wherein one or more carbon units of the hydrocarbon chain is replaced with —O—, —S—, —NR L2a —, —NR L2a C( ⁇ O)—, —C( ⁇ O)NR L2a —, —SC( ⁇ O)—, —C( ⁇ O)S—, —OC( ⁇ O)—, —C( ⁇ O)O—, —NR L2a C( ⁇ S)—, —C( ⁇ S)NR L2a —, trans-CR L2b ⁇ CR L2b —, cis-CR L2b ⁇ CR L2b —, —C ⁇ C—, —S( ⁇ O) 2 O—, —OS( ⁇ O) 2 —, —S( ⁇ O) 2 NR L2a —, or —NR L2a S( ⁇ O) 2 —.
  • R L2a is H. In certain embodiments, R L2a is substituted alkyl. In certain embodiments, R L2a is unsubstituted alkyl. In certain embodiments, R L2a is C 1-6 alkyl. In certain embodiments, R L2a is methyl. In certain embodiments, R L2a is ethyl. In certain embodiments, R L2a is propyl. In certain embodiments, R L2a is butyl. In certain embodiments, R L2a is a nitrogen protecting group. In certain embodiments, R L2a is Bn, BOC, Cbz, Fmoc, trifluoroacetyl, triphenylmethyl, or Ts.
  • At least one R L2b is H. In certain embodiments, at least one R L2b is halogen. In certain embodiments, at least one R L2b is F. In certain embodiments, at least one R L2b is Cl. In certain embodiments, at least one R L2b is Br. In certain embodiments, at least one R L2b is I (iodine). In certain embodiments, at least one R L2b is substituted alkyl. In certain embodiments, at least one R L2b is unsubstituted alkyl. In certain embodiments, at least one R L2b is C 1-6 alkyl. In certain embodiments, at least one R L2b is methyl.
  • At least one R L2b is ethyl. In certain embodiments, at least one R L2b is propyl. In certain embodiments, at least one R L2b is butyl. In certain embodiments, at least one R L2b is substituted alkenyl. In certain embodiments, at least one R L2b is unsubstituted alkenyl. In certain embodiments, at least one R L2b is vinyl. In certain embodiments, at least one R L2b is substituted alkynyl. In certain embodiments, at least one R L2b is unsubstituted alkynyl. In certain embodiments, at least one R L2b is ethynyl.
  • At least one R L2b is substituted carbocyclyl. In certain embodiments, at least one R L2b is unsubstituted carbocyclyl. In certain embodiments, at least one R L2b is substituted heterocyclyl. In certain embodiments, at least one R L2b is unsubstituted heterocyclyl. In certain embodiments, at least one R L2b is substituted aryl. In certain embodiments, at least one R L2b is unsubstituted aryl. In certain embodiments, at least one R L2b is substituted phenyl. In certain embodiments, at least one R L2b is unsubstituted phenyl.
  • At least one R L2b is substituted heteroaryl. In certain embodiments, at least one R L2b is unsubstituted heteroaryl. In certain embodiments, at least one R L2b is substituted pyridyl. In certain embodiments, at least one R L2b is unsubstituted pyridyl. In certain embodiments, two R L2b groups are joined to form a substituted carbocyclic ring. In certain embodiments, two R L2b groups are joined to form an unsubstituted carbocyclic ring. In certain embodiments, two R L2b groups are joined to form a substituted heterocyclic ring. In certain embodiments, two R L2b groups are joined to form an unsubstituted heterocyclic ring.
  • Ring C is a para-phenylene moiety. Ring C may be unsubstituted or substituted with one or more substituents R C .
  • at least one R C is H. In certain embodiments, at least one R C is halogen. In certain embodiments, at least one R C is F. In certain embodiments, at least one R C is Cl. In certain embodiments, at least one R C is Br. In certain embodiments, at least one R C is I (iodine). In certain embodiments, at least one R C is acyl. In certain embodiments, at least one R C is acetyl. In certain embodiments, at least one R C is substituted alkyl. In certain embodiments, at least one R C is unsubstituted alkyl.
  • At least one R C is C 1-6 alkyl. In certain embodiments, at least one R C is methyl. In certain embodiments, at least one R C is ethyl. In certain embodiments, at least one R C is propyl. In certain embodiments, at least one R C is butyl. In certain embodiments, at least one R C is substituted alkenyl. In certain embodiments, at least one R C is unsubstituted alkenyl. In certain embodiments, at least one R C is substituted alkynyl. In certain embodiments, at least one R C is unsubstituted alkynyl. In certain embodiments, at least one R C is substituted carbocyclyl.
  • At least one R C is unsubstituted carbocyclyl. In certain embodiments, at least one R C is substituted heterocyclyl. In certain embodiments, at least one R C is unsubstituted heterocyclyl. In certain embodiments, at least one R C is substituted aryl. In certain embodiments, at least one R C is unsubstituted aryl. In certain embodiments, at least one R C is substituted phenyl. In certain embodiments, at least one R C is unsubstituted phenyl. In certain embodiments, at least one R C is substituted heteroaryl. In certain embodiments, at least one R C is unsubstituted heteroaryl.
  • At least one R C is substituted pyridyl. In certain embodiments, at least one R C is unsubstituted pyridyl. In certain embodiments, at least one R C is —OR C1 . In certain embodiments, at least one R C is —N(R C1 ) 2 . In certain embodiments, at least one R C is SR C1 .
  • R C when R C is —OR C1 , —N(R C1 ) 2 , or —SR C1 , at least one R C1 is H. In certain embodiments, at least one R C1 is acyl. In certain embodiments, at least one R C1 is acetyl. In certain embodiments, at least one R C1 is substituted alkyl. In certain embodiments, at least one R C1 is unsubstituted alkyl. In certain embodiments, at least one R C1 is C 1-6 alkyl. In certain embodiments, at least one R C1 is methyl. In certain embodiments, at least one R C1 is ethyl. In certain embodiments, at least one R C1 is propyl.
  • At least one R C1 is butyl. In certain embodiments, at least one R C1 is substituted alkenyl. In certain embodiments, at least one R C1 is unsubstituted alkenyl. In certain embodiments, at least one R C1 is substituted alkynyl. In certain embodiments, at least one R C1 is unsubstituted alkynyl. In certain embodiments, at least one R C1 is substituted carbocyclyl. In certain embodiments, at least one R C1 is unsubstituted carbocyclyl. In certain embodiments, at least one R C1 is substituted heterocyclyl. In certain embodiments, at least one R C1 is unsubstituted heterocyclyl.
  • At least one R C1 is substituted aryl. In certain embodiments, at least one R C1 is unsubstituted aryl. In certain embodiments, at least one R C1 is substituted phenyl. In certain embodiments, at least one R C1 is unsubstituted phenyl. In certain embodiments, at least one R C1 is substituted heteroaryl. In certain embodiments, at least one R C1 is unsubstituted heteroaryl. In certain embodiments, at least one R C1 is substituted pyridyl. In certain embodiments, at least one R C1 is unsubstituted pyridyl.
  • At least one R C1 is a nitrogen protecting group when attached to a nitrogen atom. In certain embodiments, at least one R C1 is an oxygen protecting group when attached to an oxygen atom. In certain embodiments, at least one R C1 is a sulfur protecting group when attached to a sulfur atom. In certain embodiments, two R C1 groups are joined to form a substituted heterocyclic ring. In certain embodiments, two R C1 groups are joined to form an unsubstituted heterocyclic ring.
  • Ring C may be unsubstituted or substituted with one or more R C . In certain embodiments, Ring C is unsubstituted, and thus n is 0. In certain embodiments, n is 1. In certain embodiments, n is 2. In certain embodiments, n is 3. In certain embodiments, n is 4.
  • R C is substituted alkyl; and n is 1. In certain embodiments, R C is unsubstituted alkyl; and n is 1.
  • Ring D is a meta-phenylene moiety. Ring D may be unsubstituted or substituted with one or more substituents R D .
  • at least one R D is H.
  • at least one R D is halogen.
  • at least one R D is F.
  • at least one R D is Cl.
  • at least one R D is Br.
  • at least one R D is I (iodine).
  • at least one R D is acyl.
  • at least one R D is acetyl.
  • at least one R D is substituted alkyl. In certain embodiments, at least one R D is unsubstituted alkyl.
  • At least one R D is C 1-6 alkyl. In certain embodiments, at least one R D is methyl. In certain embodiments, at least one R D is ethyl. In certain embodiments, at least one R D is propyl. In certain embodiments, at least one R D is butyl. In certain embodiments, at least one R D is substituted alkenyl. In certain embodiments, at least one R D is unsubstituted alkenyl. In certain embodiments, at least one R D is substituted alkynyl. In certain embodiments, at least one R D is unsubstituted alkynyl. In certain embodiments, at least one R D is substituted carbocyclyl.
  • At least one R D is unsubstituted carbocyclyl. In certain embodiments, at least one R D is substituted heterocyclyl. In certain embodiments, at least one R D is unsubstituted heterocyclyl. In certain embodiments, at least one R D is substituted aryl. In certain embodiments, at least one R D is unsubstituted aryl. In certain embodiments, at least one R D is substituted phenyl. In certain embodiments, at least one R D is unsubstituted phenyl. In certain embodiments, at least one R D is substituted heteroaryl. In certain embodiments, at least one R D is unsubstituted heteroaryl.
  • At least one R D is substituted pyridyl. In certain embodiments, at least one R D is unsubstituted pyridyl. In certain embodiments, at least one R D is —OR D1 . In certain embodiments, at least one R D is —N(—R D1 ) 2 . In certain embodiments, at least one R D is —SR D1 .
  • At least one R D1 is H. In certain embodiments, at least one R D1 is acyl. In certain embodiments, at least one R D1 is acetyl. In certain embodiments, at least one R D1 is substituted alkyl. In certain embodiments, at least one R D1 is unsubstituted alkyl. In certain embodiments, at least one R D1 is C 1-6 alkyl. In certain embodiments, at least one R D1 is methyl. In certain embodiments, at least one R D1 is ethyl. In certain embodiments, at least one R D1 is propyl. In certain embodiments, at least one R D1 is butyl. In certain embodiments, at least one R D1 is substituted alkenyl.
  • At least one R D1 is unsubstituted alkenyl. In certain embodiments, at least one R D1 is substituted alkynyl. In certain embodiments, at least one R D1 is unsubstituted alkynyl. In certain embodiments, at least one R D1 is substituted carbocyclyl. In certain embodiments, at least one R D1 is unsubstituted carbocyclyl. In certain embodiments, at least one R D1 is substituted heterocyclyl. In certain embodiments, at least one R D1 is unsubstituted heterocyclyl. In certain embodiments, at least one R D1 is substituted aryl.
  • At least one R D1 is unsubstituted aryl. In certain embodiments, at least one R D1 is substituted phenyl. In certain embodiments, at least one R D1 is unsubstituted phenyl. In certain embodiments, at least one R D1 is substituted heteroaryl. In certain embodiments, at least one R D1 is unsubstituted heteroaryl. In certain embodiments, at least one R D1 is substituted pyridyl. In certain embodiments, at least one R D1 is unsubstituted pyridyl. In certain embodiments, at least one R D1 is a nitrogen protecting group when attached to a nitrogen atom.
  • At least one R D1 is an oxygen protecting group when attached to an oxygen atom. In certain embodiments, at least one R D1 is a sulfur protecting group when attached to a sulfur atom. In certain embodiments, two R D1 groups are joined to form a substituted heterocyclic ring. In certain embodiments, two R D1 groups are joined to form an unsubstituted heterocyclic ring.
  • Ring D may be unsubstituted or substituted with one or more R D .
  • Ring D is unsubstituted, and thus p is 0.
  • p is 1.
  • p is 2.
  • p is 3.
  • p is 4.
  • R D is substituted alkyl; and p is 1. In certain embodiments, R D is unsubstituted alkyl; and p is 1.
  • R E is a substituent on Ring D, meta to L 2 .
  • R E is:
  • R E is a group selected from the group consisting of:
  • L 3 is a divalent linker moiety.
  • L 3 may contain 0-4 carbon or hetero atoms in the backbone of L 3 .
  • L 3 may be saturated or unsaturated.
  • L 3 may be substituted or unsubstituted.
  • L 3 may be branched or unbranched.
  • L 3 is a bond.
  • L 3 is —O—.
  • L 3 is —S—.
  • L 3 is —NR L3a —.
  • L 3 is —NH—.
  • L 3 is —NR L3a C( ⁇ O)—.
  • L 3 is —NHC( ⁇ O)—.
  • L 3 is —C( ⁇ O)NR L3a —. In certain embodiments, L 3 is —C( ⁇ O)NH—. In certain embodiments, L 3 is —SC( ⁇ O)—. In certain embodiments, L 3 is —C( ⁇ O)S—. In certain embodiments, L 3 is —OC( ⁇ O)—. In certain embodiments, L 3 is —C( ⁇ O)O—. In certain embodiments, L 3 is NR L3a C( ⁇ S)—. In certain embodiments, L 3 is —NHC( ⁇ S)—. In certain embodiments, L 3 is C( ⁇ S)NR L3a —. In certain embodiments, L 3 is —C( ⁇ S)NH—.
  • L 3 is trans-CR L3b ⁇ CR L3b —. In certain embodiments, L 3 is trans-CH ⁇ CH—. In certain embodiments, L 3 is cis-CR L3b ⁇ CR L3b —. In certain embodiments, L 3 is cis-CH ⁇ CH—. In certain embodiments, L 3 is —C ⁇ C—. In certain embodiments, L 3 is —OC(R L3b ) 2 —. In certain embodiments, L 3 is —OCH 2 —. In certain embodiments, L 3 is —C(R L3b ) 2 O—. In certain embodiments, L 3 is —CH 2 O—.
  • L 3 is —NR L3a C(R L3b ) 2 —. In certain embodiments, L 3 is —NR L3a CH 2 —. In certain embodiments, L 3 is —NHCH 2 —. In certain embodiments, L 3 is —C(R L3b ) 2 NR L3a —. In certain embodiments, L 3 is —CH 2 NR L3a —. In certain embodiments, L 3 is —CH 2 NH—. In certain embodiments, L 3 is —SC(R L3b ) 2 —. In certain embodiments, L 3 is —SCH 2 —. In certain embodiments, L 3 is —C(R L3b ) 2 S—.
  • L 3 is —CH 2 S—. In certain embodiments, L 3 is —S( ⁇ O) 2 O—. In certain embodiments, L 3 is —OS( ⁇ O) 2 —. In certain embodiments, L 3 is —S( ⁇ O) 2 NR L3a —. In certain embodiments, L 3 is —S( ⁇ O) 2 NH—. In certain embodiments, L 3 is —NR L3a S( ⁇ O) 2 —. In certain embodiments, L 3 is —NHS( ⁇ O) 2 —. In certain embodiments, L 3 is a substituted C 1-4 hydrocarbon chain. In certain embodiments, L 3 is an unsubstituted C 1-4 hydrocarbon chain.
  • L 3 is a substituted C 2 hydrocarbon chain. In certain embodiments, L 3 is an unsubstituted C 2 hydrocarbon chain. In certain embodiments, L 3 is a substituted C 3 hydrocarbon chain. In certain embodiments, L 3 is an unsubstituted C 3 hydrocarbon chain. In certain embodiments, L 3 is a substituted C 4 hydrocarbon chain. In certain embodiments, L 3 is an unsubstituted C 4 hydrocarbon chain.
  • L 3 is an optionally substituted C 1-4 hydrocarbon chain, wherein one or more carbon units of the hydrocarbon chain is replaced with —O—, —S—, —NR L3a —, —NR L3a C( ⁇ O)—, —C( ⁇ O)NR L3a , —SC( ⁇ O)—, —C( ⁇ O)S—, —OC( ⁇ O)—, —C( ⁇ O)O—, —NR L3a C( ⁇ S)—, —C( ⁇ S)NR L3a —, trans-CR L3b ⁇ CR L3b —, cis-CR L3b ⁇ CR L3b —, —C ⁇ C—, —S( ⁇ O) 2 O—, —OS( ⁇ O) 2 —, S—( ⁇ O) 2 NR L3a —, or —NR L3a S( ⁇ O) 2 —.
  • R L3a is H. In certain embodiments, R L3a is substituted alkyl. In certain embodiments, R L3a is unsubstituted alkyl. In certain embodiments, R L3a is C 1-6 alkyl. In certain embodiments, R L3a is methyl. In certain embodiments, R L3a is ethyl. In certain embodiments, R L3a is propyl. In certain embodiments, R L3a is butyl. In certain embodiments, R L3a is a nitrogen protecting group. In certain embodiments, R L3a is Bn, BOC, Cbz, Fmoc, trifluoroacetyl, triphenylmethyl, or Ts.
  • At least one R L3b is H. In certain embodiments, at least one R L3b is halogen. In certain embodiments, at least one R L3b is F. In certain embodiments, at least one R L3b is Cl. In certain embodiments, at least one R L3b is Br. In certain embodiments, at least one R L3b is I (iodine). In certain embodiments, at least one R L3b is substituted alkyl. In certain embodiments, at least one R L3b is unsubstituted alkyl. In certain embodiments, at least one R L3b is C 1-6 alkyl. In certain embodiments, at least one R L3b is methyl.
  • At least one R L3b is ethyl. In certain embodiments, at least one R L3b is propyl. In certain embodiments, at least one R L3b is butyl. In certain embodiments, at least one R L3b is substituted alkenyl. In certain embodiments, at least one R L3b is unsubstituted alkenyl. In certain embodiments, at least one R L3b is vinyl. In certain embodiments, at least one R L3b is substituted alkynyl. In certain embodiments, at least one R L3b is unsubstituted alkynyl. In certain embodiments, at least one R L3b is ethynyl.
  • At least one R L3b is substituted carbocyclyl. In certain embodiments, at least one R L3b is unsubstituted carbocyclyl. In certain embodiments, at least one R L3b is substituted heterocyclyl. In certain embodiments, at least one R L3b is unsubstituted heterocyclyl. In certain embodiments, at least one R L3b is substituted aryl. In certain embodiments, at least one R L3b is unsubstituted aryl. In certain embodiments, at least one R L3b is substituted phenyl. In certain embodiments, at least one R L3b is unsubstituted phenyl.
  • At least one R L3b is substituted heteroaryl. In certain embodiments, at least one R L3b is unsubstituted heteroaryl. In certain embodiments, at least one R L3b is substituted pyridyl. In certain embodiments, at least one R L3b is unsubstituted pyridyl. In certain embodiments, two R L3b groups are joined to form a substituted carbocyclic ring. In certain embodiments, two R L3b groups are joined to form an unsubstituted carbocyclic ring. In certain embodiments, two R L3b groups are joined to form a substituted heterocyclic ring. In certain embodiments, two R L3b groups are joined to form an unsubstituted heterocyclic ring.
  • L 4 is a divalent linker moiety.
  • L 4 may contain 0-4 carbon or hetero atoms in the backbone of L 4 .
  • L 4 may be saturated or unsaturated.
  • L 4 may be substituted or unsubstituted.
  • L 4 may be branched or unbranched.
  • L 4 is a bond.
  • L 4 is a substituted C 1-4 hydrocarbon chain.
  • L 4 is an unsubstituted C 1-4 hydrocarbon chain.
  • L 4 is —CH 2 —.
  • L 4 is —CH 2 CH 2 —.
  • L 4 is —CH ⁇ CH—.
  • L 4 is —(CH 2 ) 3 —.
  • L 4 is —(CH 2 ) 4 —.
  • R E1 is H. In certain embodiments, R E1 is halogen. In certain embodiments, R E1 is F. In certain embodiments, R E1 is Cl. In certain embodiments, R E1 is Br. In certain embodiments, R E1 is I (iodine). In certain embodiments, R E1 is acyl. In certain embodiments, R E1 is acetyl. In certain embodiments, R E1 is substituted alkyl. In certain embodiments, R E1 is unsubstituted alkyl. In certain embodiments, R E1 is C 1-6 alkyl. In certain embodiments, R E1 is methyl. In certain embodiments, R E1 is ethyl. In certain embodiments, R E1 is propyl.
  • R E1 is butyl. In certain embodiments, R E1 is substituted alkenyl. In certain embodiments, R E1 is unsubstituted alkenyl. In certain embodiments, R E1 is substituted alkynyl. In certain embodiments, R E1 is unsubstituted alkynyl. In certain embodiments, R E1 is substituted carbocyclyl. In certain embodiments, R E1 is unsubstituted carbocyclyl. In certain embodiments, R E1 is substituted heterocyclyl. In certain embodiments, R E1 is unsubstituted heterocyclyl. In certain embodiments, R E1 is substituted aryl.
  • R E1 is unsubstituted aryl. In certain embodiments, R E1 is substituted phenyl. In certain embodiments, R E1 is unsubstituted phenyl. In certain embodiments, R E1 is substituted heteroaryl. In certain embodiments, R E1 is unsubstituted heteroaryl. In certain embodiments, R E1 is substituted pyridyl. In certain embodiments, R E1 is unsubstituted pyridyl. In certain embodiments, R E1 is —OR E1a —. In certain embodiments, R E1 is —N(R E1a ) 2 . In certain embodiments, R E1 is —SR E1a . In certain embodiments, R E1 is —CH 2 OR E1a . In certain embodiments, R E1 is —CH 2 N(R E1a ) 2 . In certain embodiments, R E1 is —CH 2 SR E1a .
  • At least one R E1a is H. In certain embodiments, at least one R E1a is acyl. In certain embodiments, at least one R E1a is acetyl. In certain embodiments, at least one R E1a is substituted alkyl. In certain embodiments, at least one R E1a is unsubstituted alkyl. In certain embodiments, at least one R E1a is C 1-6 alkyl. In certain embodiments, at least one R E1a is methyl. In certain embodiments, at least one R E1a is ethyl. In certain embodiments, at least one R E1a is propyl. In certain embodiments, at least one R E1a is butyl.
  • At least one R E1a is substituted alkenyl. In certain embodiments, at least one R E1a is unsubstituted alkenyl. In certain embodiments, at least one R E1a is substituted alkynyl. In certain embodiments, at least one R E1a is unsubstituted alkynyl. In certain embodiments, at least one R E1a is substituted carbocyclyl. In certain embodiments, at least one R E1a is unsubstituted carbocyclyl. In certain embodiments, at least one R E1a is substituted heterocyclyl. In certain embodiments, at least one R E1a is unsubstituted heterocyclyl.
  • At least one R E1a is substituted aryl. In certain embodiments, at least one R E1a is unsubstituted aryl. In certain embodiments, at least one R E1a is substituted phenyl. In certain embodiments, at least one R E1a is unsubstituted phenyl. In certain embodiments, at least one R E1a is substituted heteroaryl. In certain embodiments, at least one R E1a is unsubstituted heteroaryl. In certain embodiments, at least one R E1a is substituted pyridyl. In certain embodiments, at least one R E1a is unsubstituted pyridyl.
  • At least one R E1a is a nitrogen protecting group when attached to a nitrogen atom. In certain embodiments, at least one R E1a is an oxygen protecting group when attached to an oxygen atom. In certain embodiments, at least one R E1a is a sulfur protecting group when attached to a sulfur atom. In certain embodiments, two R E1a groups are joined to form a substituted heterocyclic ring. In certain embodiments, two R E1a groups are joined to form an unsubstituted heterocyclic ring.
  • R E2 is H. In certain embodiments, R E2 is halogen. In certain embodiments, R E2 is F. In certain embodiments, R E2 is Cl. In certain embodiments, R E2 is Br. In certain embodiments, R E2 is I (iodine). In certain embodiments, R E2 is acyl. In certain embodiments, R E2 is acetyl. In certain embodiments, R E2 is substituted alkyl. In certain embodiments, R E2 is unsubstituted alkyl. In certain embodiments, R E2 is C 1-6 alkyl. In certain embodiments, R E2 is methyl. In certain embodiments, R E2 is ethyl. In certain embodiments, R E2 is propyl.
  • R E2 is butyl. In certain embodiments, R E2 is substituted alkenyl. In certain embodiments, R E2 is unsubstituted alkenyl. In certain embodiments, R E2 is substituted alkynyl. In certain embodiments, R E2 is unsubstituted alkynyl. In certain embodiments, R E2 is substituted carbocyclyl. In certain embodiments, R E2 is unsubstituted carbocyclyl. In certain embodiments, R E2 is substituted heterocyclyl. In certain embodiments, R E2 is unsubstituted heterocyclyl. In certain embodiments, R E2 is substituted aryl.
  • R E2 is unsubstituted aryl. In certain embodiments, R E2 is substituted phenyl. In certain embodiments, R E2 is unsubstituted phenyl. In certain embodiments, R E2 is substituted heteroaryl. In certain embodiments, R E2 is unsubstituted heteroaryl. In certain embodiments, R E2 is substituted pyridyl. In certain embodiments, R E2 is unsubstituted pyridyl. In certain embodiments, R E2 is —OR E2a . In certain embodiments, R E2 is —N(R E2a ) 2 . In certain embodiments, R E2 is —SR E2a . In certain embodiments, R E2 is —CH 2 OR E2a . In certain embodiments, R E2 is —CH 2 N(R E2a ) 2 . In certain embodiments, R E2 is —CH 2 SR E2a .
  • At least one R E2a is H. In certain embodiments, at least one R E2a is acyl. In certain embodiments, at least one R E2a is acetyl. In certain embodiments, at least one R E2a is substituted alkyl. In certain embodiments, at least one R E2a is unsubstituted alkyl. In certain embodiments, at least one R E2a is C 1-6 alkyl. In certain embodiments, at least one R E2a is methyl. In certain embodiments, at least one R E2a is ethyl. In certain embodiments, at least one R E2a is propyl. In certain embodiments, at least one R E2a is butyl.
  • At least one R E2a is substituted alkenyl. In certain embodiments, at least one R E2a is unsubstituted alkenyl. In certain embodiments, at least one R E2a is substituted alkynyl. In certain embodiments, at least one R E2a is unsubstituted alkynyl. In certain embodiments, at least one R E2a is substituted carbocyclyl. In certain embodiments, at least one R E2a is unsubstituted carbocyclyl. In certain embodiments, at least one R E2a is substituted heterocyclyl. In certain embodiments, at least one R E2a is unsubstituted heterocyclyl.
  • At least one R E2a is substituted aryl. In certain embodiments, at least one R E2a is unsubstituted aryl. In certain embodiments, at least one R E2a is substituted phenyl. In certain embodiments, at least one R E2a is unsubstituted phenyl. In certain embodiments, at least one R E2a is substituted heteroaryl. In certain embodiments, at least one R E2a is unsubstituted heteroaryl. In certain embodiments, at least one R E2a is substituted pyridyl. In certain embodiments, at least one R E2a is unsubstituted pyridyl.
  • At least one R E2a is a nitrogen protecting group when attached to a nitrogen atom. In certain embodiments, at least one R E2a is an oxygen protecting group when attached to an oxygen atom. In certain embodiments, at least one R E2a is a sulfur protecting group when attached to a sulfur atom. In certain embodiments, two R E2a groups are joined to form a substituted heterocyclic ring. In certain embodiments, two R E2a groups are joined to form an unsubstituted heterocyclic ring.
  • R E3 is H. In certain embodiments, R E3 is halogen. In certain embodiments, R E3 is F. In certain embodiments, R E3 is Cl. In certain embodiments, R E3 is Br. In certain embodiments, R E3 is I (iodine). In certain embodiments, R E3 is acyl. In certain embodiments, R E3 is acetyl. In certain embodiments, R E3 is substituted alkyl. In certain embodiments, R E3 is unsubstituted alkyl. In certain embodiments, R E3 is C 1-6 alkyl. In certain embodiments, R E3 is methyl. In certain embodiments, R E3 is ethyl. In certain embodiments, R E3 is propyl.
  • R E3 is butyl. In certain embodiments, R E3 is substituted alkenyl. In certain embodiments, R E3 is unsubstituted alkenyl. In certain embodiments, R E3 is substituted alkynyl. In certain embodiments, R E3 is unsubstituted alkynyl. In certain embodiments, R E3 is substituted carbocyclyl. In certain embodiments, R E3 is unsubstituted carbocyclyl. In certain embodiments, R E3 is substituted heterocyclyl. In certain embodiments, R E3 is unsubstituted heterocyclyl. In certain embodiments, R E3 is substituted aryl.
  • R E3 is unsubstituted aryl. In certain embodiments, R E3 is substituted phenyl. In certain embodiments, R E3 is unsubstituted phenyl. In certain embodiments, R E3 is substituted heteroaryl. In certain embodiments, R E3 is unsubstituted heteroaryl. In certain embodiments, R E3 is substituted pyridyl. In certain embodiments, R E3 is unsubstituted pyridyl. In certain embodiments, R E3 is —OR E3a . In certain embodiments, R E3 is —N(R E3a ) 2 . In certain embodiments, R E3 is —SR E3a . In certain embodiments, R E3 is —CH 2 OR E3a . In certain embodiments, R E3 is —CH 2 N(R E3a ) 2 . In certain embodiments, R E3 is —CH 2 SR E3a .
  • At least one R E3a is H. In certain embodiments, at least one R E3a is acyl. In certain embodiments, at least one R E3a is acetyl. In certain embodiments, at least one R E3a is substituted alkyl. In certain embodiments, at least one R E3a is unsubstituted alkyl. In certain embodiments, at least one R E3a is C 1-6 alkyl. In certain embodiments, at least one R E3a is methyl. In certain embodiments, at least one R E3a is ethyl. In certain embodiments, at least one R E3a is propyl. In certain embodiments, at least one R E3a is butyl.
  • At least one R E3a is substituted alkenyl. In certain embodiments, at least one R E3a is unsubstituted alkenyl. In certain embodiments, at least one R E3a is substituted alkynyl. In certain embodiments, at least one R E3a is unsubstituted alkynyl. In certain embodiments, at least one R E3a is substituted carbocyclyl. In certain embodiments, at least one R E3a is unsubstituted carbocyclyl. In certain embodiments, at least one R E3a is substituted heterocyclyl. In certain embodiments, at least one R E3a is unsubstituted heterocyclyl.
  • At least one R E3a is substituted aryl. In certain embodiments, at least one R E3a is unsubstituted aryl. In certain embodiments, at least one R E3a is substituted phenyl. In certain embodiments, at least one R E3a is unsubstituted phenyl. In certain embodiments, at least one R E3a is substituted heteroaryl. In certain embodiments, at least one R E3a is unsubstituted heteroaryl. In certain embodiments, at least one R E3a is substituted pyridyl. In certain embodiments, at least one R E3a is unsubstituted pyridyl.
  • At least one R E3a is a nitrogen protecting group when attached to a nitrogen atom. In certain embodiments, at least one R E3a is an oxygen protecting group when attached to an oxygen atom. In certain embodiments, at least one R E3a is a sulfur protecting group when attached to a sulfur atom. In certain embodiments, two R E3a groups are joined to form a substituted heterocyclic ring. In certain embodiments, two R E3a groups are joined to form an unsubstituted heterocyclic ring.
  • R E may include a substituent R E4 .
  • R E4 is a leaving group.
  • R E4 is halogen.
  • R E4 is F.
  • R E4 is Cl.
  • R E4 is Br.
  • R E4 is I (iodine).
  • R E4 is —OS( ⁇ O) w R E4a .
  • w is 1.
  • w is 2.
  • R E4 is OMs.
  • R E4 is —OTf.
  • R E4 is —OTs.
  • R E4 is —OBs. In certain embodiments, R E4 is 2-nitrobenzenesulfonyloxy. In certain embodiments, R E4 is —OR E4a . In certain embodiments, R E4 is —OMe. In certain embodiments, R E4 is —OCF 3 . In certain embodiments, R E4 is —OPh. In certain embodiments, R E4 is —OC( ⁇ O)R E4a . In certain embodiments, R E4 is —OC( ⁇ O)Me. In certain embodiments, R E4 is —OC( ⁇ O)CF 3 . In certain embodiments, R E4 is —OC( ⁇ O)Ph.
  • R E4 is —OC( ⁇ O)Cl. In certain embodiments, R E4 is —OC( ⁇ O)OR E4a . In certain embodiments, R E4 is —OC( ⁇ O)OMe. In certain embodiments, R E4 is —OC( ⁇ O)O(t-Bu).
  • R E4a is substituted alkyl. In certain embodiments, R E4a is unsubstituted alkyl. In certain embodiments, R E4a is substituted alkenyl. In certain embodiments, R E4a is unsubstituted alkenyl. In certain embodiments, R E4a is substituted alkynyl. In certain embodiments, R E4a is unsubstituted alkynyl. In certain embodiments, R E4a is substituted carbocyclyl. In certain embodiments, R E4a is unsubstituted carbocyclyl. In certain embodiments, R E4a is substituted heterocyclyl. In certain embodiments, R E4a is unsubstituted heterocyclyl.
  • R E4a is substituted aryl. In certain embodiments, R E4a is unsubstituted aryl. In certain embodiments, R E4a is substituted heteroaryl. In certain embodiments, R E4a is unsubstituted heteroaryl.
  • Y is O. In certain embodiments, Y is S. In certain embodiments, Y is NR E5 . In certain embodiments, Y is NH.
  • R E5 is H. In certain embodiments, R E5 is substituted alkyl. In certain embodiments, R E5 is unsubstituted alkyl. In certain embodiments, R E5 is C 1-6 alkyl. In certain embodiments, R E5 is methyl. In certain embodiments, R E5 is ethyl. In certain embodiments, R E5 is propyl. In certain embodiments, R E5 is butyl. In certain embodiments, R E5 is a nitrogen protecting group. In certain embodiments, R E5 is BOC. In certain embodiments, R E5 is Cbz. In certain embodiments, R E5 is Fmoc. In certain embodiments, R E5 is Bn.
  • a is 1. In certain embodiments, a is 2.
  • z is 0. In certain embodiments, z is 1. In certain embodiments, z is 2. In certain embodiments, z is 3. In certain embodiments, z is 4. In certain embodiments, z is 5. In certain embodiments, z is 6.
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
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  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compound of Formula (I) is of the formula:
  • the compounds of the present invention are the compounds described herein, and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, or prodrugs thereof.
  • the compounds of the present invention are the compounds of Formula (I), and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, or prodrugs thereof.
  • the compounds of the present invention are JNK-IN-5, JNK-IN-6, JNK-IN-7, JNK-IN-8, JNK-IN-9, JNK-IN-10, JNK-IN-11, JNK-IN-12, THZ-2-117-1, THZ-2-118-1, THZ-2-140-2, THZ-2-142-1, THZ-2-143-1, THZ-2-144-1, THZ-2-145-1, THZ-2-147-1, THZ-2-148-1, THZ-3-06-1, THZ-3-07-1, THZ-3-11-1, THZ-3-30-1, THZ-3-39-1, and THZ-3-46-1, and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, or prodrugs thereof.
  • the compound of the present invention is of the formula:
  • THZ-2-071-1, ZG-9, ZG-10, ZG-6, and THZ-2-102-1 may not have significant activity against JNK; however, these compounds may be useful in inhibiting other kinases.
  • the compounds of the invention bear multiple binding motifs to JNK.
  • Ring A of the inventive compounds may be accommodated inside a hydrophobic pocket in the ATP-binding site of JNK. Functionalities on Ring A may bind to residues of JNK, such as to the “gatekeeper” methionine residue.
  • Ring B of the compounds of the invention may bind to JNK kinase hinge residues, such as Leu148 and Met149.
  • Functional groups of R E may form a hydrogen bond with JNK's Asn152 residue. This hydrogen bond may be important for positioning Ring D and orienting the Michael acceptor moiety proximal to Cys154 to facilitate covalent bond formation.
  • the compounds of the invention non-covalently bind to JNK.
  • the compounds of the invention covalently attach to JNK.
  • the covalent attachment of the compounds of the invention to JNK is irreversible. In other embodiments, the covalent attachment is reversible.
  • the present invention provides pharmaceutical compositions comprising a compound of the present invention, e.g., a compound of Formula (I), and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, and prodrugs thereof, as described herein, and optionally a pharmaceutically acceptable excipient.
  • the compound of the present invention, or a pharmaceutically acceptable salt thereof is provided in an effective amount in the pharmaceutical composition.
  • the effective amount is a therapeutically effective amount.
  • the effective amount is a prophylactically effective amount.
  • compositions described herein can be prepared by any method known in the art of pharmacology.
  • such preparatory methods include the steps of bringing the compound of the present invention (the “active ingredient”) into association with a carrier and/or one or more other accessory ingredients, and then, if necessary and/or desirable, shaping and/or packaging the product into a desired single- or multi-dose unit.
  • compositions can be prepared, packaged, and/or sold in bulk, as a single unit dose, and/or as a plurality of single unit doses.
  • a “unit dose” is a discrete amount of the pharmaceutical composition comprising a predetermined amount of the active ingredient.
  • the amount of the active ingredient is generally equal to the dosage of the active ingredient which would be administered to a subject and/or a convenient fraction of such a dosage such as, for example, one-half or one-third of such a dosage.
  • Relative amounts of the active ingredient, the pharmaceutically acceptable excipient, and/or any additional ingredients in a pharmaceutical composition of the invention will vary, depending upon the identity, size, and/or condition of the subject treated and further depending upon the route by which the composition is to be administered.
  • the composition may comprise between 0.1% and 100% (w/w) active ingredient.
  • compositions used in the manufacture of provided pharmaceutical compositions include inert diluents, dispersing and/or granulating agents, surface active agents and/or emulsifiers, disintegrating agents, binding agents, preservatives, buffering agents, lubricating agents, and/or oils. Excipients such as cocoa butter and suppository waxes, coloring agents, coating agents, sweetening, flavoring, and perfuming agents may also be present in the composition.
  • Exemplary diluents include calcium carbonate, sodium carbonate, calcium phosphate, dicalcium phosphate, calcium sulfate, calcium hydrogen phosphate, sodium phosphate lactose, sucrose, cellulose, microcrystalline cellulose, kaolin, mannitol, sorbitol, inositol, sodium chloride, dry starch, cornstarch, powdered sugar, and mixtures thereof.
  • Exemplary granulating and/or dispersing agents include potato starch, corn starch, tapioca starch, sodium starch glycolate, clays, alginic acid, guar gum, citrus pulp, agar, bentonite, cellulose, and wood products, natural sponge, cation-exchange resins, calcium carbonate, silicates, sodium carbonate, cross-linked poly(vinyl-pyrrolidone) (crospovidone), sodium carboxymethyl starch (sodium starch glycolate), carboxymethyl cellulose, cross-linked sodium carboxymethyl cellulose (croscarmellose), methylcellulose, pregelatinized starch (starch 1500), microcrystalline starch, water insoluble starch, calcium carboxymethyl cellulose, magnesium aluminum silicate (Veegum), sodium lauryl sulfate, quaternary ammonium compounds, and mixtures thereof.
  • crospovidone cross-linked poly(vinyl-pyrrolidone)
  • sodium carboxymethyl starch sodium starch glycolate
  • Exemplary surface active agents and/or emulsifiers include natural emulsifiers (e.g. acacia, agar, alginic acid, sodium alginate, tragacanth, chondrux, cholesterol, xanthan, pectin, gelatin, egg yolk, casein, wool fat, cholesterol, wax, and lecithin), colloidal clays (e.g. bentonite (aluminum silicate) and Veegum (magnesium aluminum silicate)), long chain amino acid derivatives, high molecular weight alcohols (e.g.
  • natural emulsifiers e.g. acacia, agar, alginic acid, sodium alginate, tragacanth, chondrux, cholesterol, xanthan, pectin, gelatin, egg yolk, casein, wool fat, cholesterol, wax, and lecithin
  • colloidal clays e.g. bentonite (aluminum silicate) and Veegum (mag
  • stearyl alcohol cetyl alcohol, oleyl alcohol, triacetin monostearate, ethylene glycol distearate, glyceryl monostearate, and propylene glycol monostearate, polyvinyl alcohol), carbomers (e.g. carboxy polymethylene, polyacrylic acid, acrylic acid polymer, and carboxyvinyl polymer), carrageenan, cellulosic derivatives (e.g. carboxymethylcellulose sodium, powdered cellulose, hydroxymethyl cellulose, hydroxypropyl cellulose, hydroxypropyl methylcellulose, methylcellulose), sorbitan fatty acid esters (e.g.
  • polyoxyethylene sorbitan monolaurate Tween 20
  • polyoxyethylene sorbitan Tween 60
  • polyoxyethylene sorbitan monooleate Tween 80
  • sorbitan monopalmitate Span 40
  • sorbitan monostearate Span 60
  • sorbitan tristearate Span 65
  • polyoxyethylene esters e.g. polyoxyethylene monostearate (Myrj 45), polyoxyethylene hydrogenated castor oil, polyethoxylated castor oil, polyoxymethylene stearate, and Solutol
  • sucrose fatty acid esters e.g.
  • CremophorTM polyoxyethylene ethers, (e.g. polyoxyethylene lauryl ether (Brij 30)), poly(vinyl-pyrrolidone), diethylene glycol monolaurate, triethanolamine oleate, sodium oleate, potassium oleate, ethyl oleate, oleic acid, ethyl laurate, sodium lauryl sulfate, Pluronic F 68, Poloxamer 188, cetrimonium bromide, cetylpyridinium chloride, benzalkonium chloride, docusate sodium, and/or mixtures thereof.
  • polyoxyethylene ethers e.g. polyoxyethylene lauryl ether (Brij 30)
  • poly(vinyl-pyrrolidone) diethylene glycol monolaurate
  • triethanolamine oleate sodium oleate
  • potassium oleate ethyl oleate
  • oleic acid ethyl laurate
  • Exemplary binding agents include starch (e.g. cornstarch and starch paste), gelatin, sugars (e.g. sucrose, glucose, dextrose, dextrin, molasses, lactose, lactitol, mannitol, etc.), natural and synthetic gums (e.g.
  • acacia sodium alginate, extract of Irish moss, panwar gum, ghatti gum, mucilage of isapol husks, carboxymethylcellulose, methylcellulose, ethylcellulose, hydroxyethylcellulose, hydroxypropyl cellulose, hydroxypropyl methylcellulose, microcrystalline cellulose, cellulose acetate, poly(vinyl-pyrrolidone), magnesium aluminum silicate (Veegum), and larch arabogalactan), alginates, polyethylene oxide, polyethylene glycol, inorganic calcium salts, silicic acid, polymethacrylates, waxes, water, alcohol, and/or mixtures thereof.
  • Exemplary preservatives include antioxidants, chelating agents, antimicrobial preservatives, antifungal preservatives, alcohol preservatives, acidic preservatives, and other preservatives.
  • antioxidants include alpha tocopherol, ascorbic acid, acorbyl palmitate, butylated hydroxyanisole, butylated hydroxytoluene, monothioglycerol, potassium metabisulfite, propionic acid, propyl gallate, sodium ascorbate, sodium bisulfite, sodium metabisulfite, and sodium sulfite.
  • Exemplary chelating agents include ethylenediaminetetraacetic acid (EDTA) and salts and hydrates thereof (e.g., sodium edetate, disodium edetate, trisodium edetate, calcium disodium edetate, dipotassium edetate, and the like), citric acid and salts and hydrates thereof (e.g., citric acid monohydrate), fumaric acid and salts and hydrates thereof, malic acid and salts and hydrates thereof, phosphoric acid and salts and hydrates thereof, and tartaric acid and salts and hydrates thereof.
  • EDTA ethylenediaminetetraacetic acid
  • salts and hydrates thereof e.g., sodium edetate, disodium edetate, trisodium edetate, calcium disodium edetate, dipotassium edetate, and the like
  • citric acid and salts and hydrates thereof e.g., citric acid mono
  • antimicrobial preservatives include benzalkonium chloride, benzethonium chloride, benzyl alcohol, bronopol, cetrimide, cetylpyridinium chloride, chlorhexidine, chlorobutanol, chlorocresol, chloroxylenol, cresol, ethyl alcohol, glycerin, hexetidine, imidurea, phenol, phenoxyethanol, phenylethyl alcohol, phenylmercuric nitrate, propylene glycol, and thimerosal.
  • antifungal preservatives include butyl paraben, methyl paraben, ethyl paraben, propyl paraben, benzoic acid, hydroxybenzoic acid, potassium benzoate, potassium sorbate, sodium benzoate, sodium propionate, and sorbic acid.
  • Exemplary alcohol preservatives include ethanol, polyethylene glycol, phenol, phenolic compounds, bisphenol, chlorobutanol, hydroxybenzoate, and phenylethyl alcohol.
  • Exemplary acidic preservatives include vitamin A, vitamin C, vitamin E, beta-carotene, citric acid, acetic acid, dehydroacetic acid, ascorbic acid, sorbic acid, and phytic acid.
  • preservatives include tocopherol, tocopherol acetate, deteroxime mesylate, cetrimide, butylated hydroxyanisol (BHA), butylated hydroxytoluened (BHT), ethylenediamine, sodium lauryl sulfate (SLS), sodium lauryl ether sulfate (SLES), sodium bisulfite, sodium metabisulfite, potassium sulfite, potassium metabisulfite, Glydant Plus, Phenonip, methylparaben, Germall 115, Germaben II, Neolone, Kathon, and Euxyl.
  • the preservative is an anti-oxidant.
  • the preservative is a chelating agent.
  • Exemplary buffering agents include citrate buffer solutions, acetate buffer solutions, phosphate buffer solutions, ammonium chloride, calcium carbonate, calcium chloride, calcium citrate, calcium glubionate, calcium gluceptate, calcium gluconate, D-gluconic acid, calcium glycerophosphate, calcium lactate, propanoic acid, calcium levulinate, pentanoic acid, dibasic calcium phosphate, phosphoric acid, tribasic calcium phosphate, calcium hydroxide phosphate, potassium acetate, potassium chloride, potassium gluconate, potassium mixtures, dibasic potassium phosphate, monobasic potassium phosphate, potassium phosphate mixtures, sodium acetate, sodium bicarbonate, sodium chloride, sodium citrate, sodium lactate, dibasic sodium phosphate, monobasic sodium phosphate, sodium phosphate mixtures, tromethamine, magnesium hydroxide, aluminum hydroxide, alginic acid, pyrogen-free water, isotonic saline, Ringer
  • Exemplary lubricating agents include magnesium stearate, calcium stearate, stearic acid, silica, talc, malt, glyceryl behanate, hydrogenated vegetable oils, polyethylene glycol, sodium benzoate, sodium acetate, sodium chloride, leucine, magnesium lauryl sulfate, sodium lauryl sulfate, and mixtures thereof.
  • Exemplary natural oils include almond, apricot kernel, avocado, babassu, bergamot, black current seed, borage, cade, camomile, canola, caraway, carnauba, castor, cinnamon, cocoa butter, coconut, cod liver, coffee, corn, cotton seed, emu, eucalyptus, evening primrose, fish, flaxseed, geraniol, gourd, grape seed, hazel nut, hyssop, isopropyl myristate, jojoba, kukui nut, lavandin, lavender, lemon, litsea cubeba, macademia nut, mallow, mango seed, meadowfoam seed, mink, nutmeg, olive, orange, orange roughy, palm, palm kernel, peach kernel, peanut, poppy seed, pumpkin seed, rapeseed, rice bran, rosemary, safflower, sandalwood, sasquana, savoury, sea buckt
  • Exemplary synthetic oils include, but are not limited to, butyl stearate, caprylic triglyceride, capric triglyceride, cyclomethicone, diethyl sebacate, dimethicone 360, isopropyl myristate, mineral oil, octyldodecanol, oleyl alcohol, silicone oil, and mixtures thereof.
  • Liquid dosage forms for oral and parenteral administration include pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs.
  • the liquid dosage forms may comprise inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethylformamide, oils (e.g., cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof.
  • inert diluents commonly used in the art such as, for example, water or other solvents, so
  • the oral compositions can include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents.
  • adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents.
  • the conjugates of the invention are mixed with solubilizing agents such as CremophorTM, alcohols, oils, modified oils, glycols, polysorbates, cyclodextrins, polymers, and mixtures thereof.
  • sterile injectable aqueous or oleaginous suspensions can be formulated according to the known art using suitable dispersing or wetting agents and suspending agents.
  • the sterile injectable preparation can be a sterile injectable solution, suspension or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a solution in 1,3-butanediol.
  • acceptable vehicles and solvents that can be employed are water, Ringer's solution, U.S.P. and isotonic sodium chloride solution.
  • sterile, fixed oils are conventionally employed as a solvent or suspending medium.
  • any bland fixed oil can be employed including synthetic mono- or diglycerides.
  • fatty acids such as oleic acid are used in the preparation of injectables.
  • the injectable formulations can be sterilized, for example, by filtration through a bacterial-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.
  • compositions for rectal or vaginal administration are typically suppositories which can be prepared by mixing the conjugates of this invention with suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active ingredient.
  • suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active ingredient.
  • Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules.
  • the active ingredient is mixed with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate or dicalcium phosphate and/or (a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid, (b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, (c) humectants such as glycerol, (d) disintegrating agents such as agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate, (e) solution retarding agents such as paraffin, (f) absorption accelerators such as quaternary ammonium compounds, (g) wetting agents such as, for example, cetyl alcohol and glycerol mono
  • Solid compositions of a similar type can be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like.
  • the solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings and other coatings well known in the pharmaceutical formulating art. They may optionally comprise opacifying agents and can be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions which can be used include polymeric substances and waxes.
  • Solid compositions of a similar type can be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polethylene glycols and the like.
  • the active ingredient can be in micro-encapsulated form with one or more excipients as noted above.
  • the solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings, release controlling coatings and other coatings well known in the pharmaceutical formulating art.
  • the active ingredient can be admixed with at least one inert diluent such as sucrose, lactose or starch.
  • Such dosage forms may comprise, as is normal practice, additional substances other than inert diluents, e.g., tableting lubricants and other tableting aids such a magnesium stearate and microcrystalline cellulose.
  • the dosage forms may comprise buffering agents. They may optionally comprise opacifying agents and can be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner.
  • opacifying agents include polymeric substances and waxes.
  • Dosage forms for topical and/or transdermal administration of a compound of this invention may include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants and/or patches.
  • the active ingredient is admixed under sterile conditions with a pharmaceutically acceptable carrier and/or any needed preservatives and/or buffers as can be required.
  • the present invention contemplates the use of transdermal patches, which often have the added advantage of providing controlled delivery of an active ingredient to the body.
  • Such dosage forms can be prepared, for example, by dissolving and/or dispensing the active ingredient in the proper medium.
  • the rate can be controlled by either providing a rate controlling membrane and/or by dispersing the active ingredient in a polymer matrix and/or gel.
  • Suitable devices for use in delivering intradermal pharmaceutical compositions described herein include short needle devices such as those described in U.S. Pat. Nos. 4,886,499; 5,190,521; 5,328,483; 5,527,288; 4,270,537; 5,015,235; 5,141,496; and 5,417,662.
  • Intradermal compositions can be administered by devices which limit the effective penetration length of a needle into the skin, such as those described in PCT publication WO 99/34850 and functional equivalents thereof.
  • Jet injection devices which deliver liquid vaccines to the dermis via a liquid jet injector and/or via a needle which pierces the stratum corneum and produces a jet which reaches the dermis are suitable.
  • Jet injection devices are described, for example, in U.S. Pat. Nos. 5,480,381; 5,599,302; 5,334,144; 5,993,412; 5,649,912; 5,569,189; 5,704,911; 5,383,851; 5,893,397; 5,466,220; 5,339,163; 5,312,335; 5,503,627; 5,064,413; 5,520,639; 4,596,556; 4,790,824; 4,941,880; 4,940,460; and PCT publications WO 97/37705 and WO 97/13537.
  • Ballistic powder/particle delivery devices which use compressed gas to accelerate vaccine in powder form through the outer layers of the skin to the dermis are suitable.
  • conventional syringes can be used in the classical mantoux method of intradermal administration.
  • Formulations suitable for topical administration include, but are not limited to, liquid and/or semi liquid preparations such as liniments, lotions, oil in water and/or water in oil emulsions such as creams, ointments and/or pastes, and/or solutions and/or suspensions.
  • Topically-administrable formulations may, for example, comprise from about 1% to about 10% (w/w) active ingredient, although the concentration of the active ingredient can be as high as the solubility limit of the active ingredient in the solvent.
  • Formulations for topical administration may further comprise one or more of the additional ingredients described herein.
  • a pharmaceutical composition of the invention can be prepared, packaged, and/or sold in a formulation suitable for pulmonary administration via the buccal cavity.
  • a formulation may comprise dry particles which comprise the active ingredient and which have a diameter in the range from about 0.5 to about 7 nanometers or from about 1 to about 6 nanometers.
  • Such compositions are conveniently in the form of dry powders for administration using a device comprising a dry powder reservoir to which a stream of propellant can be directed to disperse the powder and/or using a self propelling solvent/powder dispensing container such as a device comprising the active ingredient dissolved and/or suspended in a low-boiling propellant in a sealed container.
  • Such powders comprise particles wherein at least 98% of the particles by weight have a diameter greater than 0.5 nanometers and at least 95% of the particles by number have a diameter less than 7 nanometers. Alternatively, at least 95% of the particles by weight have a diameter greater than 1 nanometer and at least 90% of the particles by number have a diameter less than 6 nanometers.
  • Dry powder compositions may include a solid fine powder diluent such as sugar and are conveniently provided in a unit dose form.
  • Low boiling propellants generally include liquid propellants having a boiling point of below 65° F. at atmospheric pressure. Generally the propellant may constitute 50 to 99.9% (w/w) of the composition, and the active ingredient may constitute 0.1 to 20% (w/w) of the composition.
  • the propellant may further comprise additional ingredients such as a liquid non-ionic and/or solid anionic surfactant and/or a solid diluent (which may have a particle size of the same order as particles comprising the active ingredient).
  • compositions of the invention formulated for pulmonary delivery may provide the active ingredient in the form of droplets of a solution and/or suspension.
  • Such formulations can be prepared, packaged, and/or sold as aqueous and/or dilute alcoholic solutions and/or suspensions, optionally sterile, comprising the active ingredient, and may conveniently be administered using any nebulization and/or atomization device.
  • Such formulations may further comprise one or more additional ingredients including, but not limited to, a flavoring agent such as saccharin sodium, a volatile oil, a buffering agent, a surface active agent, and/or a preservative such as methylhydroxybenzoate.
  • the droplets provided by this route of administration may have an average diameter in the range from about 0.1 to about 200 nanometers.
  • Formulations described herein as being useful for pulmonary delivery are useful for intranasal delivery of a pharmaceutical composition of the invention.
  • Another formulation suitable for intranasal administration is a coarse powder comprising the active ingredient and having an average particle from about 0.2 to 500 micrometers. Such a formulation is administered by rapid inhalation through the nasal passage from a container of the powder held close to the nares.
  • Formulations for nasal administration may, for example, comprise from about as little as 0.1% (w/w) and as much as 100% (w/w) of the active ingredient, and may comprise one or more of the additional ingredients described herein.
  • a pharmaceutical composition of the invention can be prepared, packaged, and/or sold in a formulation for buccal administration.
  • Such formulations may, for example, be in the form of tablets and/or lozenges made using conventional methods, and may contain, for example, 0.1 to 20% (w/w) active ingredient, the balance comprising an orally dissolvable and/or degradable composition and, optionally, one or more of the additional ingredients described herein.
  • formulations for buccal administration may comprise a powder and/or an aerosolized and/or atomized solution and/or suspension comprising the active ingredient.
  • Such powdered, aerosolized, and/or aerosolized formulations when dispersed, may have an average particle and/or droplet size in the range from about 0.1 to about 200 nanometers, and may further comprise one or more of the additional ingredients described herein.
  • a pharmaceutical composition of the invention can be prepared, packaged, and/or sold in a formulation for ophthalmic administration.
  • Such formulations may, for example, be in the form of eye drops including, for example, a 0.1/1.0% (w/w) solution and/or suspension of the active ingredient in an aqueous or oily liquid carrier.
  • Such drops may further comprise buffering agents, salts, and/or one or more other of the additional ingredients described herein.
  • Other opthalmically-administrable formulations which are useful include those which comprise the active ingredient in microcrystalline form and/or in a liposomal preparation. Ear drops and/or eye drops are contemplated as being within the scope of this invention.
  • compositions suitable for administration to humans are principally directed to pharmaceutical compositions which are suitable for administration to humans, it will be understood by the skilled artisan that such compositions are generally suitable for administration to animals of all sorts. Modification of pharmaceutical compositions suitable for administration to humans in order to render the compositions suitable for administration to various animals is well understood, and the ordinarily skilled veterinary pharmacologist can design and/or perform such modification with ordinary experimentation.
  • compositions of the present invention are typically formulated in dosage unit form for ease of administration and uniformity of dosage. It will be understood, however, that the total daily usage of the compositions of the present invention will be decided by the attending physician within the scope of sound medical judgment.
  • the specific therapeutically effective dose level for any particular subject or organism will depend upon a variety of factors including the disease being treated and the severity of the disorder; the activity of the specific active ingredient employed; the specific composition employed; the age, body weight, general health, sex and diet of the subject; the time of administration, route of administration, and rate of excretion of the specific active ingredient employed; the duration of the treatment; drugs used in combination or coincidental with the specific active ingredient employed; and like factors well known in the medical arts.
  • the compounds and compositions provided herein can be administered by any route, including enteral (e.g., oral), parenteral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, subcutaneous, intraventricular, transdermal, interdermal, rectal, intravaginal, intraperitoneal, topical (as by powders, ointments, creams, and/or drops), mucosal, nasal, bucal, sublingual; by intratracheal instillation, bronchial instillation, and/or inhalation; and/or as an oral spray, nasal spray, and/or aerosol.
  • enteral e.g., oral
  • parenteral intravenous, intramuscular, intra-arterial, intramedullary
  • intrathecal subcutaneous, intraventricular, transdermal, interdermal, rectal, intravaginal, intraperitoneal
  • topical as by powders, ointments, creams, and/or drops
  • mucosal nasal,
  • Specifically contemplated routes are oral administration, intravenous administration (e.g., systemic intravenous injection), regional administration via blood and/or lymph supply, and/or direct administration to an affected site.
  • intravenous administration e.g., systemic intravenous injection
  • regional administration via blood and/or lymph supply
  • direct administration to an affected site.
  • the most appropriate route of administration will depend upon a variety of factors including the nature of the agent (e.g., its stability in the environment of the gastrointestinal tract), and/or the condition of the subject (e.g., whether the subject is able to tolerate oral administration).
  • the exact amount of a compound required to achieve an effective amount will vary from subject to subject, depending, for example, on species, age, and general condition of a subject, severity of the side effects or disorder, identity of the particular compound(s), mode of administration, and the like.
  • the desired dosage can be delivered three times a day, two times a day, once a day, every other day, every third day, every week, every two weeks, every three weeks, or every four weeks.
  • the desired dosage can be delivered using multiple administrations (e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, or more administrations).
  • an effective amount of a compound for administration one or more times a day to a 70 kg adult human may comprise about 0.0001 mg to about 3000 mg, about 0.0001 mg to about 2000 mg, about 0.0001 mg to about 1000 mg, about 0.001 mg to about 1000 mg, about 0.01 mg to about 1000 mg, about 0.1 mg to about 1000 mg, about 1 mg to about 1000 mg, about 1 mg to about 100 mg, about 10 mg to about 1000 mg, or about 100 mg to about 1000 mg, of a compound per unit dosage form.
  • the compounds of the invention may be at dosage levels sufficient to deliver from about 0.001 mg/kg to about 100 mg/kg, from about 0.01 mg/kg to about 50 mg/kg, preferably from about 0.1 mg/kg to about 40 mg/kg, preferably from about 0.5 mg/kg to about 30 mg/kg, from about 0.01 mg/kg to about 10 mg/kg, from about 0.1 mg/kg to about 10 mg/kg, and more preferably from about 1 mg/kg to about 25 mg/kg, of subject body weight per day, one or more times a day, to obtain the desired therapeutic effect.
  • dose ranges as described herein provide guidance for the administration of provided pharmaceutical compositions to an adult.
  • the amount to be administered to, for example, a child or an adolescent can be determined by a medical practitioner or person skilled in the art and can be lower or the same as that administered to an adult.
  • a compound or composition, as described herein, can be administered in combination with one or more additional therapeutically active agents.
  • the compounds or compositions can be administered in combination with additional therapeutically active agents that improve their bioavailability, reduce and/or modify their metabolism, inhibit their excretion, and/or modify their distribution within the body.
  • additional therapeutically active agents that improve their bioavailability, reduce and/or modify their metabolism, inhibit their excretion, and/or modify their distribution within the body.
  • the therapy employed may achieve a desired effect for the same disorder, and/or it may achieve different effects.
  • the compound or composition can be administered concurrently with, prior to, or subsequent to, one or more additional therapeutically active agents.
  • each agent will be administered at a dose and/or on a time schedule determined for that agent.
  • the additional therapeutically active agent utilized in this combination can be administered together in a single composition or administered separately in different compositions.
  • the particular combination to employ in a regimen will take into account compatibility of the inventive compound with the additional therapeutically active agent and/or the desired therapeutic effect to be achieved.
  • additional therapeutically active agents utilized in combination be utilized at levels that do not exceed the levels at which they are utilized individually. In some embodiments, the levels utilized in combination will be lower than those utilized individually.
  • Exemplary additional therapeutically active agents include, but are not limited to, anti-cancer agents, anti-diabetic agents, anti-inflammatory agents, immunosuppressant agents, and a pain-relieving agent.
  • Therapeutically active agents include small organic molecules such as drug compounds (e.g., compounds approved by the U.S.
  • CFR Code of Federal Regulations
  • proteins proteins, carbohydrates, monosaccharides, oligosaccharides, polysaccharides, nucleoproteins, mucoproteins, lipoproteins, synthetic polypeptides or proteins, small molecules linked to proteins, glycoproteins, steroids, nucleic acids, DNAs, RNAs, nucleotides, nucleosides, oligonucleotides, antisense oligonucleotides, lipids, hormones, vitamins, and cells.
  • CFR Code of Federal Regulations
  • kits e.g., pharmaceutical packs.
  • the kits provided may comprise an inventive pharmaceutical composition or compound and a container (e.g., a vial, ampule, bottle, syringe, and/or dispenser package, or other suitable container).
  • a container e.g., a vial, ampule, bottle, syringe, and/or dispenser package, or other suitable container.
  • provided kits may optionally further include a second container comprising a pharmaceutical excipient for dilution or suspension of an inventive pharmaceutical composition or compound.
  • the inventive pharmaceutical composition or compound provided in the container and the second container are combined to form one unit dosage form.
  • kits for preventing and/or treating a disease of a subject include a first container comprising a compound, or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, prodrug, and composition thereof; and an instruction for administering the compound, or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, prodrug, and composition thereof, to a subject to prevent or treat a JNK-associated disease.
  • the kits include a first container comprising a JNK inhibitor.
  • kits include a first container comprising an irreversible JNK inhibitor. In certain embodiments, the kits include a first container comprising a compound of the present invention. In certain embodiments, the kits include a first container comprising a compound of the present invention. In certain embodiments, the kits include a first container comprising a compound described herein. In certain embodiments, the kits include a first container comprising a compound selected from the group consisting of JNK-IN-5, JNK-IN-6, JNK-IN-7, JNK-IN-8, JNK-IN-9, JNK-IN-10, JNK-IN-11, and JNK-IN-12.
  • kits include a first container comprising a compound selected from the group consisting of THZ-2-117-1, THZ-2-118-1, THZ-2-140-2, THZ-2-142-1, THZ-2-143-1, THZ-2-144-1, THZ-2-145-1, THZ-2-147-1, THZ-2-148-1, THZ-3-06-1, THZ-3-07-1, THZ-3-11-1, THZ-3-30-1, THZ-3-39-1, and THZ-3-46-1.
  • kits are used for preventing and/or treating diseases associated with JNK kinase activity. In certain embodiments, the kits are used for preventing and/or treating a proliferative disease. In certain embodiments, the kits are used for preventing and/or treating cancer. In certain embodiments, the kits are used for preventing and/or treating a benign neoplasm. In certain embodiments, the kits are used for preventing and/or treating a neurodegenerative disease. In certain embodiments, the kits are used for preventing and/or treating a metabolic disorder. In certain embodiments, the kits are used for preventing and/or treating an inflammatory disease. In certain embodiments, the kits are used for preventing and/or treating a cardiovascular disease.
  • the present invention provides methods for the prevention and treatment of various diseases, e.g., neurodegenerative diseases, metabolic disorders, inflammatory diseases, cardiovascular diseases, and proliferative diseases (e.g., cancer and benign neoplasms).
  • various diseases e.g., neurodegenerative diseases, metabolic disorders, inflammatory diseases, cardiovascular diseases, and proliferative diseases (e.g., cancer and benign neoplasms).
  • the methods of the present invention comprise administering to a subject in need thereof an effective amount of a compound of the present invention, or a pharmaceutical composition thereof.
  • the effective amount is a therapeutically effective amount. In certain embodiments, the effective amount is a prophylactically effective amount.
  • the subject administered the inventive compound, or composition as described herein is an animal.
  • the animal may be of either sex and may be of any stage of development.
  • the animal is a mammal.
  • the subject is a human.
  • the subject is a domesticated animal, such as a dog, cat, cow, pig, horse, sheep, or goat.
  • the subject is a companion animal such as a dog or cat.
  • the subject is a livestock animal such as a cow, pig, horse, sheep, or goat.
  • the subject is a zoo animal.
  • the subject is a research animal such as a rodent (e.g., mouse, rat), dog, pig, or non-human primate.
  • a rodent e.g., mouse, rat
  • dog e.g., dog
  • pig e.g., dog
  • pig e.g., dog
  • pig e.g., dog
  • pig e.g., dog
  • pig e.g., a non-human primate
  • the subject is a non-human, genetically engineered animal.
  • the subject is a non-human transgenic animal, such as a transgenic mouse or transgenic pig.
  • the disease is a proliferative disease, e.g., cancer.
  • the disease is benign neoplasm.
  • the disease is a neurodegenerative disease.
  • the disease is stroke.
  • the disease is Parkinson's disease.
  • the disease is Alzheimer's disease.
  • the disease is a metabolic disorder.
  • the disease is diabetes.
  • the disease is an inflammatory disease.
  • the disease is a cardiovascular disease, e.g., stroke.
  • the methods of the present invention comprise administering to a subject with a proliferative disease (e.g., cancer) an effective amount of a compound of the present invention, or the pharmaceutical composition thereof.
  • a proliferative disease e.g., cancer
  • exemplary cancers include, but are not limited to, acoustic neuroma; adenocarcinoma; adrenal gland cancer; anal cancer; angiosarcoma (e.g., lymphangiosarcoma, lymphangioendotheliosarcoma, hemangiosarcoma); appendix cancer; benign monoclonal gammopathy; biliary cancer (e.g., cholangiocarcinoma); bladder cancer; breast cancer (e.g., adenocarcinoma of the breast, papillary carcinoma of the breast, mammary cancer, medullary carcinoma of the breast); brain cancer [e.g., meningioma, glioblastomas, glioma (e
  • liver cancer e.g., hepatocellular cancer (HCC), malignant hepatoma
  • lung cancer e.g., bronchogenic carcinoma, small cell lung cancer (SCLC), non-small cell lung cancer (NSCLC), adenocarcinoma of the lung
  • leiomyosarcoma LMS
  • mastocytosis e.g., systemic mastocytosis
  • muscle cancer myelodysplastic syndrome (MDS); mesothelioma; myeloproliferative disorder (MPD) (e.g., polycythemia vera (PV), essential thrombocytosis (ET), agnogenic myeloid metaplasia (AMM) a.k.a.
  • myelofibrosis MF
  • chronic idiopathic myelofibrosis chronic myelocytic leukemia (CML), chronic neutrophilic leukemia (CNL), hypereosinophilic syndrome (HES)
  • neuroblastoma e.g., neurofibromatosis (NF) type 1 or type 2, schwannomatosis
  • neuroendocrine cancer e.g., gastroenteropancreatic neuroendoctrine tumor (GEP-NET), carcinoid tumor
  • osteosarcoma e.g., bone cancer
  • ovarian cancer e.g., cystadenocarcinoma, ovarian embryonal carcinoma, ovarian adenocarcinoma
  • papillary adenocarcinoma pancreatic cancer
  • pancreatic cancer e.g., pancreatic andenocarcinoma, intraductal papillary mucinous neoplasm (IPMN), Islet cell tumors
  • the methods of the present invention comprise administering to a subject with a benign neoplasm an effective amount of a compound of the present invention, or the pharmaceutical composition thereof.
  • the methods of the present invention comprise administering to a subject with a neurodegenerative disease an effective amount of a compound of the present invention, or the pharmaceutical composition thereof.
  • exemplary neurodegenerative diseases include, but are not limited to, multiple sclerosis, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, Alzheimer's disease.
  • the methods of the present invention comprise administering to a subject with Parkinson's disease an effective amount of a compound of the present invention, or the pharmaceutical composition thereof.
  • the methods of the present invention comprise administering to a subject with Alzheimer's disease an effective amount of a compound of the present invention, or the pharmaceutical composition thereof.
  • the methods of the present invention comprise administering to a subject with a metabolic disorder (e.g., Type I or II diabetes, or an obesity-related condition or complication thereof) an effective amount of a compound of the present invention, or the pharmaceutical composition thereof.
  • a metabolic disorder e.g., Type I or II diabetes, or an obesity-related condition or complication thereof
  • An “obesity-related condition” as used herein includes, but is not limited to, a condition related to obesity, undesired weight gain (e.g., from medication-induced weight gain, from cessation of smoking) or an over-eating disorder (e.g., binge eating, bulimia, compulsive eating, or a lack of appetite control each of which can optionally lead to undesired weight gain or obesity).
  • Obesity and “obese” as used herein refers to class I obesity, class II obesity, class III obesity and pre-obesity (e.g., being “over-weight”) as defined by the World health Organization.
  • Obesity-related conditions include, but are not limited to, Type II diabetes mellitus; ischemic heart disease, arterial vascular disease, angina, myocardial infarction, strobe, migraines, congestive heart failure, deep vein thrombosis, pulmonary embolism, gall stones, gastroesophageal reflux disease, obesity hyperventilation syndrome, erectile dysfunction, urinary incontinence, liver injury, and chronic renal failure.
  • the metabolic disorder is diabetes.
  • the methods of the present invention comprise administering to a subject with diabetes (i.e., Type I or II diabetes) an effective amount of a compound of the present invention, or the pharmaceutical composition thereof.
  • the methods of the present invention comprise administering to a subject with an inflammatory disease an effective amount of a compound of the present invention, or the pharmaceutical composition thereof.
  • Inflammatory disease refers to those diseases, disorders or conditions that are characterized by signs of pain (dolor, from the generation of noxious substances and the stimulation of nerves), heat (calor, from vasodilatation), redness (rubor, from vasodilatation and increased blood flow), swelling (tumor, from excessive inflow or restricted outflow of fluid), and/or loss of function (functio laesa, which can be partial or complete, temporary or permanent.
  • Inflammation takes on many forms and includes, but is not limited to, acute, adhesive, atrophic, catarrhal, chronic, cirrhotic, diffuse, disseminated, exudative, fibrinous, fibrosing, focal, granulomatous, hyperplastic, hypertrophic, interstitial, metastatic, necrotic, obliterative, parenchymatous, plastic, productive, proliferous, pseudomembranous, purulent, sclerosing, seroplastic, serous, simple, specific, subacute, suppurative, toxic, traumatic, and/or ulcerative inflammation.
  • Exemplary inflammatory diseases include, but are not limited to, inflammation associated with acne, anemia (e.g., aplastic anemia, haemolytic autoimmune anaemia), asthma, arteritis (e.g., polyarteritis, temporal arteritis, periarteritis nodosa, Takayasu's arteritis), arthritis (e.g., crystalline arthritis, osteoarthritis, psoriatic arthritis, gouty arthritis, reactive arthritis, rheumatoid arthritis and Reiter's arthritis), ankylosing spondylitis, amylosis, amyotrophic lateral sclerosis, autoimmune diseases, allergies or allergic reactions, atherosclerosis, bronchitis, bursitis, chronic prostatitis, conjunctivitis, Chagas disease, chronic obstructive pulmonary disease, cermatomyositis, diverticulitis, diabetes (e.g., type I diabetes mellitus, type 2 diabetes mell
  • the methods of the present invention comprise administering to a subject with a cardiovascular disease an effective amount of a compound of the present invention, or the pharmaceutical composition thereof.
  • cardiovascular diseases include, but are not limited to, hypertension, circulatory shock, myocardial reperfusion injury, stroke, and atherosclerosis.
  • the methods of the present invention comprise administering to a subject with stroke an effective amount of a compound of the present invention, or the pharmaceutical composition thereof.
  • the disease is a disease associated with JNK activity, e.g., a disease associated with aberrant or unwanted JNK activity.
  • the disease results from increased JNK activity.
  • the methods of the present invention comprise administering to a subject with a JNK-associated disease an effective amount of a compound of the present invention, or a pharmaceutical composition thereof.
  • Inhibition of JNK1 is associated with treatment of cancer, diabetes, and inflammatory diseases (e.g., inflammation).
  • Increased JNK1 activity is also associated with obesity, i.e., inhibition of JNK1 or mouse knockout has been found to increase insulin sensitivity.
  • Inhibition of JNK3 is associated with the treatment of neurodegenerative diseases. See Kyriakis et al., 2001; Zhang et al., 2005; and Hunot et al., 2004 for discussions of the association of JNK with various neurodegenerative diseases, e.g., Parkinson's and Alzheimer's diseases.
  • CDK7 is also called CDK catalytic kinase which usually catalyze the CDK1 and CDK2 for the phosphorylation of their substrate.
  • CDK1 and CDK2 they are activated in many cancers, e.g., colon cancer, liver cancer, and breast cancer.
  • CDK7 is known to be responsible at least for RNAP II Ser 2 and Ser 5 phosphorylation.
  • CDK7 has a lysine which has a very similar location as cysteine in JNK, and it envisioned that active JNK inhibitors of the present invention will also be active CDK7 inhibitors.
  • the methods of the present invention comprise administering to a subject with a CDK7-associated disease an effective amount of a compound of the present invention, or a pharmaceutical composition thereof.
  • the methods of the present invention comprise administering to a subject with an IRAK1/4-associated disease an effective amount of a compound of the present invention, or a pharmaceutical composition thereof.
  • the methods of the present invention comprise administering to a subject with an EGFR-associated disease an effective amount of a compound of the present invention, or a pharmaceutical composition thereof.
  • the methods of the present invention comprise administering to a subject with a DDR1/2-associated disease an effective amount of a compound of the present invention, or a pharmaceutical composition thereof.
  • the methods of the present invention comprise administering to a subject with a c-Kit-associated disease an effective amount of a compound of the present invention, or a pharmaceutical composition thereof.
  • the methods of the present invention comprise administering to a subject with a PDGFR-associated disease an effective amount of a compound of the present invention, or a pharmaceutical composition thereof.
  • a proliferative disease may also be associated with inhibition of apoptosis of a cell in a biological sample or subject. All types of biological samples described herein or known in the art are contemplated as being within the scope of the invention. Apoptosis is the process of programmed cell death. Inhibition of apoptosis may result in uncontrolled cell proliferation and, therefore, may cause proliferative diseases.
  • the present invention provides methods of inhibiting cell growth in a biological sample or subject by contacting with the biological sample or administering to the subject an effective amount of a compound of the present invention, or a pharmaceutical composition thereof.
  • the present invention provides methods of inducing apoptosis of a cell in a biological sample or a subject by contacting with the biological sample or administering to the subject an effective amount of a compound of the present invention, or a pharmaceutical composition thereof.
  • the cell described herein may be an abnormal cell.
  • the cell may be in vitro or in vivo.
  • the cell is a proliferative cell.
  • the cell is a blood cell.
  • the cell is a lymphocyte.
  • the cell is a cancer cell.
  • the cell is a benign neoplastic cell.
  • the cell is an endothelial cell.
  • the cell is an immune cell.
  • the compound is a JNK inhibitor. In certain embodiments, the compound is a JNK1 inhibitor. In certain embodiments, the compound is a JNK2 inhibitor. In certain embodiments, the compound is a JNK3 inhibitor. In certain embodiments, the compound is a CDK7 inhibitor. In certain embodiments, the compound is an IRAK1/4 inhibitor. In certain embodiments, the compound is an EGFR inhibitor. In certain embodiments, the compound is a DDR1/2 inhibitor. In certain embodiments, the compound is a c-Kit inhibitor. In certain embodiments, the compound is a PDGFR inhibitor.
  • the compound is a compound of the present invention.
  • Another aspect of the invention relates to methods of screening a library of compounds to identify one or more compounds that are useful in the treatment of a proliferative disease, in inhibiting cell growth, and/or in inducing apoptosis of a cell.
  • the library of compounds is a library of compounds of the present invention.
  • the methods of screening a library include providing at least two different compounds of the present invention, or pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, or prodrugs thereof, or pharmaceutical compositions thereof; and performing at least one assay using the different compounds of the present invention, or pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, or prodrugs thereof, or pharmaceutical compositions thereof, to detect one or more characteristics.
  • the methods of screening a library include providing at least two different compounds of the present invention, or pharmaceutically acceptable salts thereof, or pharmaceutical compositions thereof; and performing at least one assay using the different compounds of the present invention, or pharmaceutically acceptable salts thereof, or pharmaceutical compositions thereof, to detect one or more characteristics.
  • the characteristic is a characteristic associated with proliferative diseases.
  • the characteristic is a desired characteristic.
  • the desired characteristic is usefulness in treating a proliferative disease, in inhibiting cell growth or cell proliferation, and/or in inducing apoptosis of a cell.
  • the desired characteristic is anti-proliferation.
  • the desired characteristic is anti-cancer.
  • the desired characteristic is inhibition of a kinase. In certain embodiments, the desired characteristic is inhibition of JNK. In certain embodiments, the desired characteristic is inhibition of CDK7. In certain embodiments, the desired characteristic is inhibition of IRAK1/4. In certain embodiments, the desired characteristic is inhibition of EGFR. In certain embodiments, the desired characteristic is inhibition of DDR1/2. In certain embodiments, the desired characteristic is inhibition of c-Kit. In certain embodiments, the desired characteristic is inhibition of PDGFR.
  • the characteristic to be detected may also be an undesired characteristic associated with the proliferative disease, cell growth or cell proliferation, and/or apoptosis of a cell. In certain embodiments, the undesired characteristic is induction of cell growth or cell proliferation. In certain embodiments, the undesired characteristic is inhibition of apoptosis of a cell.
  • the different compounds of the present invention may be provided from natural sources (see, e.g., Sternberg et al., Proc. Nat. Acad. Sci. USA , (1995) 92:1609-1613) or generated by synthetic methods such as combinatorial chemistry (see, e.g., Ecker et al., Bio/Technology , (1995) 13:351-360 and U.S. Pat. No. 5,571,902).
  • the different compounds are provided by liquid-phase or solution synthesis.
  • the different compounds are provided by solid-phase synthesis.
  • the different compounds are provided by a high-throughput, parallel, or combinatorial synthesis.
  • the different compounds are provided by a low-throughput synthesis. In certain embodiments, the different compounds are provided by a one-pot synthesis. The different compounds may be provided robotically or manually.
  • the step of providing at least two different compounds of the present invention include arraying into at least two vessels at least two different compounds of the present invention wherein the compounds are bound to solid supports, cleaving the compounds from the solid supports, and dissolving the cleaved compounds in a solvent.
  • the solid supports include, but do not limit to, beads (e.g., resin beads and magnetic beads), hollow fibers, solid fibers, plates, dishes, flasks, meshes, screens, and membranes. In certain embodiments, the solid supports are beads.
  • one solid support is capable of supporting at least 50 nmol of a compound. In certain embodiments, one solid support is capable of supporting at least 100 nmol of a compound. In certain embodiments, one solid support is capable of supporting at least 200 nmol of a compound.
  • Each vessel may contain one or more support-bound compounds of the present invention. In certain embodiments, each vessel contains one support-bound compounds of the present invention.
  • the solid supports and/or the compounds may be labeled with one or more labeling agents for the identification or detection of the compounds.
  • the vessels may be wells of a microtiter plate.
  • the solvent may be an inorganic solvent, organic solvent, or a mixture thereof. The steps of arraying, cleaving, and dissolving may be performed robotically or manually.
  • the methods of screening a library of compounds involve at least one assay.
  • the assay is performed to detect one or more characteristics associated with the proliferative disease described herein.
  • the assay may be an immunoassay, such as a sandwich-type assay, competitive binding assay, one-step direct test, two-step test, or blot assay.
  • the step of performing at least one assay may be performed robotically or manually.
  • the activity of a kinase is inhibited.
  • the activity of JNK is inhibited.
  • the activity of CDK is inhibited.
  • the activity of CDK7 is inhibited.
  • the expression of a kinase, such as JNK and CDK (e.g., CDK7), is down-regulated.
  • apoptosis of a cell is induced.
  • Another aspect of the present invention relates to compounds described therein, or pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, or compositions thereof, for use in treating a proliferative disease in a subject in need thereof.
  • Still another aspect of the present invention relates to compounds described therein, or pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, or compositions thereof, for use in inhibiting cell growth in a biological sample or subject in need thereof.
  • the present invention provides compounds described therein, or pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, or compositions thereof, for use in inducing apoptosis of a cell in a biological sample or subject in need thereof.
  • protecting groups may be necessary to prevent certain functional groups from undergoing undesired reactions.
  • suitable protecting group for a particular functional group as well as suitable conditions for protection and deprotection are well known in the art. For example, numerous protecting groups, and their introduction and removal, are described in Greene et al., Protecting Groups in Organic Synthesis , Second Edition, Wiley, New York, 1991, and references cited therein.
  • Each of the compounds shown in Scheme 1 may be designated a different compound number.
  • Table 1 illustrates the alternative compound designation numbers of these compounds.
  • JNK-IN-5 and THZ-2-117-1 are alternative compound numbers designating the same compound.
  • the nitro compound obtained from a reaction of the aniline and nitrobenzoyl chloride was suspended in ethyl acetate/methanol (5:1) and treated with SnCl 2 (2.5 equiv.). After stirring for 2-5 h at 80° C., the reaction mixture was cooled to room temperature and poured into saturated aqueous NaHCO 3 . The mixture was stirred for 10 min and the aqueous phase was then extracted with chloroform and 2-propanol (4:1). The combined organic layer was washed with water and brine, dried over MgSO 4 , filtered through a pad of celite and concentrated under reduced pressure. The resulting crude product was purified by flash column chromatography with CH 2 Cl 2 /methanol (10/1) to provide the title compound.
  • JNK protein +/ ⁇ inhibitor JNK-IN-7
  • a self-packed reversed phase column 1/32′′ O.D. ⁇ 500 ⁇ m I.D., 5 cm of POROS 10R2 resin.
  • the QTRAP was operated in Q1 MS mode at unit resolution scanning at 2000 amu/sec.
  • LTQ OrbitrapMS spectra were acquired in centroid mode using the electron multipliers for ion detection. Mass spectra were deconvoluted using MagTran 1.03b2 software.
  • JNK-IN-7 treated JNK (25 ⁇ g, about 620 pmol) was diluted with ammonium bicarbonate buffer at pH 8.0 and then reduced for 30 min at 56° C. with 10 mM DTT. After cooling for 5 min, the protein was alkylated with 22.5 mM iodoacetamide for 30 min at room temperature in the dark and digested overnight with 1.5 ⁇ g of trypsin at 37° C. In the morning, 1 ⁇ g of Glu-C was added, and the solution further incubated at 37° C. for 8 hr.
  • MS 2 mass spectrometer
  • the cell based kinase assays for c-Jun phosphorylation carried out by using the LanthaScreenTM c-Jun (1-79) HeLa cell line (Life Technologies, Carlsbad, Calif.) which stably express GFP-c-Jun 1-79 and GFP-ATF2 19-106, respectively. Phosphorylation was determined by measuring the time resolved FRET (TR-FRET) between a terbium labeled phospho-c-Jun specific antibody and GFP.
  • TR-FRET time resolved FRET
  • the cells were plated in white tissue culture treated 384 well plates at a density of 10,000 cell per well in 32 ⁇ L assay medium (Opti-MEM®, supplemented with 0.5% charcoal/dextran-treated FBS, 100 U/ml penicillin and 100 ⁇ g/ml streptomycin, 0.1 mM nonessential amino acids, 1 mM sodium pyruvate, 25 mM Hepes, pH 7.3, and lacking phenol red). After overnight incubation, cells were pretreated for 90 minutes with compound (at indicated concentration) diluted in 4 ⁇ L assay buffer followed by 30 min of stimulation with 5 ng/ml of TNF- ⁇ , in 4 ⁇ L assay buffer (final assay volume was 40 ⁇ l).
  • Opti-MEM® supplemented with 0.5% charcoal/dextran-treated FBS, 100 U/ml penicillin and 100 ⁇ g/ml streptomycin, 0.1 mM nonessential amino acids, 1 mM sodium pyruvate, 25 mM Hepe
  • the medium was then removed by aspiration, and the cells were lysed by adding 20 ⁇ l of lysis buffer (20 mM Tris-HCl, pH 7.6, 5 mM EDTA, 1% Nonidet P-40 substitute, 5 mM NaF, 150 mM NaCl, and 1:100 protease and phosphatase inhibitor mix, SIGMA P8340 and P2850, respectively).
  • the lysis buffer included 2 nM of the terbium-labeled anti-c-Jun (pSer73) detection antibodies (Life Technologies).
  • Cells were plated at 7500 cells/well in 96-well microscopy plates (Corning) in recommended media for 24 hours, and then starved in media lacking serum for 16 hours. Cells were pre-treated for 180 minutes with 10-fold stock solutions of JNK inhibitors and for 10 min with control compounds MK2206, PD0325901, SB239063, KIN040, and KIN208 and treated with 10-fold stock solutions of IGF-1, IL-6, TNF- ⁇ (all PeproTech), or anisomycin for 60 minutes. Cells were fixed in 2% paraformaldehyde for 10 min at room temperature and washed with PBS-T (Phosphate Buffered Saline, 0.1% Tween 20).
  • PBS-T Phosphate Buffered Saline, 0.1% Tween 20
  • Cells were permeabilized in methanol for 10 min at room temperature, washed with PBS-T, and blocked in Odyssey Blocking Buffer (LI-COR Biosciences) for 1 hour at room temperature. Cells were incubated overnight at 4° C. with antibody specific for Erk1/2(pT202/pY204), Akt(pS473), c-Jun(pS73), pP38(T180/Y182) and pSTAT3(Y705) (Cell Signaling Technology), pRSK1(S380) and pMSK1(S376) (Epitomics), and NF- ⁇ B (Santa Cruz Biotechnology) diluted 1:400 in Odyssey Blocking Buffer.
  • Odyssey Blocking Buffer LI-COR Biosciences
  • Cells were washed three times in PBS-T and incubated with rabbit-specific secondary antibody labeled with Alexa Fluor 647 (Invitrogen) diluted 1:2000 in Odyssey Blocking Buffer. Cells were washed once in PBS-T and once in PBS and incubated in 250 ng/ml Hoechst 33342 (Invitrogen) and 1:1000 Whole Cell Stain (blue; Thermo Scientific) solution. Cells were washed twice with PBS and imaged in an imageWoRx high-throughput microscope (Applied Precision). Data were plotted using DataPflex.
  • A375 cells (ATCC® CRL-1619TM) were pre-treated with 1 ⁇ M compound for the indicated amounts of time. Remove the medium and wash 3 times with PBS. Resuspend the cell pellet with 1 mL Lysis Buffer (1% NP-40, 1% CHAPS, 25 mM Tris, 150 mM NaCl, Phosphatase Inhibitor Cocktail, Roche 04906845001, and Protease Inhibitor Cocktail Roche 11836170001). Rotate end-to-end for 30 min at 4° C. Lysates were cleared by centrifugation at 14000 rpm for 15 min in the Eppendorf.
  • Lysis Buffer 1% NP-40, 1% CHAPS, 25 mM Tris, 150 mM NaCl, Phosphatase Inhibitor Cocktail, Roche 04906845001, and Protease Inhibitor Cocktail Roche 1183617000.
  • the cleared lysates gel filtered into Kinase Buffer (0.1% NP-40, 20 mM HEPES, 150 mM NaCl, Phosphatase Inhibitor Cocktail, and Protease Inhibitor Cocktail) using Bio-Rad 10DG columns.
  • the total protein concentration of the gel-filtered lysate should be around 5-15 mg/ml.
  • Cell lysate was labeled with the probe from ActivX® at 5 ⁇ M for 1 hour. Samples were reduced with DTT, and cysteines were blocked with iodoacetamide and gel filtered to remove excess reagents and exchange the buffer.
  • Lysis Buffer contained 50 mM Tris/HCl (pH 7.5), 1 mM EGTA, 1 mM EDTA, 1% (w/v) 1 mM sodium orthovanadate, 10 mM sodium (3-glycerophosphate, 50 mM NaF, 5 mM sodium pyrophosphate, 0.27 M sucrose, 1 mM Benzamidine, and 2 mM phenylmethanesulphonylfluoride (PMSF) and supplemented with 1% (v/v) Triton X-100.
  • Kinase assay buffer contained 50 mM Tris/HCl (pH 7.5) and 0.1 mM EGTA.
  • HEK-293 cells stably expressing Interleukin Receptor 1 were cultured in Dulbecco's Modified Eagle's medium (DMEM) supplemented with 10% FBS, 2 mM glutamine and 1 ⁇ antimycotic/antibiotic solution.
  • DMEM Dulbecco's Modified Eagle's medium
  • FBS FBS
  • 2 mM glutamine 1 ⁇ antimycotic/antibiotic solution.
  • Cells were serum starved for 18 h before incubation with DMSO or different inhibitors, stimulated with 2 ⁇ M anisomycin (Sigma) for 1 h, and lysates were clarified by centrifugation for 10 min at 16000 g and 4° C.
  • Cell lysates (30 ⁇ g) were resolved by electrophoresis on SDS polyacrylamide gels (10%) or Novex 4-12% gradient gels, and electroblotted to nitrocellulose membranes.
  • Membranes were blocked with 5% skimmed milk (w/v) in 50 mM Tris/HCl (pH 7.5) 0.15 M NaCl, and 0.1% (v/v) Tween (TBST Buffer).
  • Primary antibodies were used at a concentration of 1 ⁇ g/ml, diluted in 5% skimmed milk in TBST, and incubated overnight at 4° C. Detection of immune-complexes was performed using horseradish-peroxidase-conjugated secondary antibodies (Pierce) and an enhanced-chemiluminescence reagent (in-house).
  • Wild type JNK2 or mutant JNK2[Cys116Ser] was activated in a reaction mixture containing 2 ⁇ M JNK2, 200 nM MKK4, 200 nM MKK7 in kinase assay buffer containing 0.1 mM ATP, and 10 mM magnesium chloride. After incubation at 30 min at 30° C. the reaction mixture was snap frozen in aliquots.
  • JNK2 Activity of JNK2 was assessed in a total reaction volume of 50 ⁇ l containing 200 nM activated wild type JNK or mutant JNK2[Cys116Ser], in kinase buffer containing 0.1 mM [ ⁇ -32P]ATP (about 500-1000 cpm/pmol), 10 mM magnesium chloride, and 2 ⁇ M ATF2 (residues 19-96) as a substrate. Reactions were terminated by adding 20 mM EDTA. 40 ⁇ l of the reaction mixture was applied to P81 phosphocellulose paper which was washed in 50 mM phosphoric acid and phosphorylated ATF2 peptide bound to p81 paper quantified by Cerenkov counting.
  • the JNK family of kinases constitutes a central node in the stress-activated MAPK signaling pathway and may provide potential targets for future drugs to treat cancer, inflammatory diseases and neurological diseases.
  • a 9 L analogue Figure 1; Crocker et al., 2011
  • achieving pharmacological inhibition of JNK in animal models has to a large extent been hampered by the lack of potent and selective inhibitors with suitable pharmacokinetic properties.
  • irreversible JNK inhibitors are developed that covalently modify a conserved cysteine residue.
  • sustained target inhibition can be achieved with only transient exposure of the target to the inhibitor which reduces the need to achieve pharmacological properties that would allow for sustained drug levels in vivo (Singh et al., 2010).
  • potent inhibition is completely dependent on covalent modification and therefore mutation of the reactive cysteine residue creates a version of JNK that are insensitive to the compounds. These mutant forms of JNK can then be used to establish the JNK-dependency of any observed inhibitor induced phenotype which provides a powerful control for specificity.
  • Cysteine-directed covalent inhibitors possess a number of potential advantages relative to non-covalent inhibitors such as ability to control kinase selectivity using both non-covalent and covalent recognition of the kinase and the ability to exhibit prolonged pharmacodynamics despite competition with high endogenous intracellular ATP concentrations.
  • cysteine positions have been targeted in the ATP-site and there are at least 180 kinases that possess a cysteine that could theoretically be targeted by suitably designed inhibitors (Zhang et al., 2009).
  • provided in the present invention include the structure-based design, detailed biochemical and cellular characterization, and crystal structure analysis of JNK3 modified by covalent inhibitors that can irreversibly modify a conserved cysteine residue in JNK.
  • cysteine-directed covalent inhibitors are from the “type-1” (Liu et al., 2006) inhibitor class: they bind to the kinase in an “active” conformation with the activation loop in a conformation conducive to substrate binding. It is speculated whether “type-2” inhibitors which bind kinases in an “inactive” state with the activation loop in a conformation that blocks substrate from binding might also present a promising platform from which to design a new class of covalent inhibitors.
  • FIG. 2A Measurement of the distance between methylpiperidine moiety of imatinib and Cys788 in c-Kit (PDB: 1T46) (Mol et al., 2004) ( FIG. 2A ) inspired the effort to replace the methylpiperzine moiety with an electrophilic acrylamide bearing a water-solubility enhancing dimethylamino group to generate JNK-IN-7 ( FIG. 3 ). It was confirmed that these binding results translated into single digit micromolar IC 50 for inhibition of JNK kinase activity using the “Z”-lyte assay format (Table 2).
  • JNK-IN-6 was prepared with an unreactive and approximately isosteric propyl amide group replacing the acrylamide of JNK-IN-5. As expected, this compound exhibited an almost 100-fold less potent biochemical IC 50 on JNK1, 2, and 3 (Table 2).
  • a small collection of analogs of JNK-IN-7 bearing modifications was prepared that was expected to influence the selectivity relative to other kinases. Also prepared were three methylated analogs JNK-IN-8, JNK-IN-9, and JNK-IN-10, all of which retained the ability to potently inhibit JNK biochemical activity.
  • JNK-IN-7 The pyridine ring of JNK-IN-7 was replaced with substituents that had previously been reported in other JNK inhibitors including a bulky group 2-phenylpyrazolo[1,5-a]pyridine (Alam et al., 2007) and benzothiazol-2-yl acetonitrile (Gaillard et al., 2005). The influence of these changes on kinase selectivity is discussed in detail below.
  • JNK-IN-7 was co-crystallized with JNK3 de novo using the same JNK3 protein reported previously for 9 L (Kamenecka et al., 2010) ( FIG. 6 and Table 3).
  • the resulting 2.60 ⁇ and 2.97 ⁇ crystal structures were in good agreement with the docking model described above.
  • Continuous electron density was visible to Cys154 consistent with covalent bond formation ( FIG. 7 ).
  • the inhibitor formed three hydrogen bonds with JNK3, two from the aminopyrimidine motif to the kinase hinge residues Leu148 and Met149 and a third from the amide NH to Asn152.
  • This third hydrogen bond may be important for positioning the terminal ring and orienting the acrylamide moiety proximal to Cys 154 thereby facilitating covalent bond formation.
  • the overall kinase conformation of JNK is remarkably similar to the reported 9 L crystal structure (average RSMD 2.40 ⁇ ) (Kamenecka et al., 2010) with the kinase assuming an active conformation. This demonstrates that the covalent inhibitor does not appear to trap an unusual conformation of the kinase. There is a small hydrophobic pocket adjacent to the aniline ortho position which may explain why there was tolerance for the “flag” methyl group in JNK-IN-8 which provided a crucial selectivity determinant.
  • the pyridine moiety binds in a hydrophobic pocket and did not optimally fill this space which was consistent with the potency improvements realized by replacement with the larger moieties present in JNK-IN-11 and JNK-IN-12. Modification of the inhibitor in this region would clearly afford significant opportunities for modulating both inhibitor potency and selectivity.
  • R cryst 4 ⁇ hkl ⁇ ⁇ ⁇ F obs ⁇ ( hkl ) ⁇ - ⁇ F calc ⁇ ( hkl ) ⁇ ⁇ / ⁇ hkl ⁇ ⁇ F obs ⁇ ( hkl ) ⁇
  • the first assay format is a high-throughput (HTS) compatible cellular assay capable of measuring changes in phosphorylation of c-Jun using the measurement of time resolved fluorescence resonance energy transfer (TR-FRET) between a stably expressed GFP-c-Jun (1-79) fusion protein and a terbium labeled anti pSer73 c-Jun antibody as readout (Robers et al., 2008; Carlson et al., 2009; and Stebbins et al., 2008).
  • TR-FRET time resolved fluorescence resonance energy transfer
  • the second assay format consisted of treating serum starved A375 cells with test compounds followed by stimulation of the JNK kinase pathway with anisomycin and monitoring c-Jun phosphorylation by confocal microscopy with an anti-phospho Ser73 antibody (Millard et al., 2011; and Hendriks et al., 2010). With the exception of a few compounds, both assay formats provided a similar rank-order of IC 50 's for this compound series (Table 2). In agreement with the biochemical assays, JNK-IN-5 also provided the break-through in cellular potency and was capable of inhibiting of c-Jun phosphorylation with an IC 50 of about 100 nM in HeLa cells and about 30 nM in A375 cells.
  • JNK-IN-7 the most potent cellular inhibitor of JNK activity in this series, incorporated the phenylpyrazoleo[1,5-a]pyridine motif and possessed an IC 50 of about 30 nM and about 10 nM in HeLa and A375 cells respectively.
  • JNK-IN-6 the compound incapable of covalent bond formation, possessed an IC 50 50-fold higher than its covalent analog JNK-IN-5 again underscoring the requirement for the acrylamide moiety to achieve potent cellular inhibition.
  • SP600125, 5A, and AS601245 FIG. 1
  • all these compounds exhibited IC 50 's in the micromolar range which suggests that covalent inhibition may be required to observe potent inhibition under the conditions investigated.
  • a pulse-chase assay was developed. A375 cells were treated with JNK-IN-5 for 1, 2, 3, 4, and 5 hours to allow for cell penetration and labeling of intracellular targets. Cell lysates were then prepared and labeled with ATP-biotin which contains a reactive acyl phosphate anhydride that reacts non-specifically with the catalytic lysine of kinases including JNK (Patricelli et al., 2007). Streptavidin affinity chromatography is then used to isolate all biotinylated proteins and JNK protein is detected following SDS-PAGE and Western blotting ( FIG. 8 ).
  • JNK-IN-5 The amount of time that JNK-IN-5 must be incubated with cells to fully protect JNK from subsequent labeling by ATP-biotin provides a measure of the rate of intracellular covalent bond formation. It took approximately three hours for JNK-IN-5 to modify JNK to an undetectable level by this assay format. As a negative control, the non-covalent inhibitor JNK-IN-6 was subject to the same protocol and was demonstrated to be incapable of protecting JNK from labeling by ATP-biotin.
  • the kinase selectivity of several key compounds was first evaluated using a chemical proteomic approach named KiNativ which detects 260 kinases in A375 cells (ActivX Biosciences). To probe the intracellular targets of the compounds, A375 cells were incubated with the inhibitors and then looked for protection of labeling by an ATP-biotin probe that non-specifically labels conserved lysines on kinases and other nucleotide-dependent enzymes. This provided an important advantage relative to the in vitro kinase selectivity profiling because in vitro the short incubation times and presence of reactive thiols in the buffers can potentially cause false negatives for acrylamide-modified kinase inhibitors.
  • JNK-IN-6 did not inhibit JNK activity following the same live cell treatment.
  • JNK-IN-7 also binds to IRAK1, PIP5K3, PI3KC3, and PIP4K2C. Since cysteine-directed covalent kinase inhibitors will sometimes cross-react with kinases that contain an equivalently placed cysteine, a sequence alignment was performed to identify all kinases which have a cysteine near JNK1 Cys116 ( FIG. 10 ).
  • IRAK1 exhibited a detectable binding affinity to JNK-IN-7 based upon KinomeScan profiling. Since IRAK1 crystal structure is not available, the IRAK4 crystal structure (PDB: 3CGF) was examined which demonstrates that Cys276 is potentially located in a similar location relative to the reactive Cys154 of JNK3. Therefore covalent modification of IRAK1 by JNK-IN-7 is a possibility and indeed biochemical kinase assay afforded an IC 50 of about 10 nM against IRAK1.
  • JNK-IN-7 inhibited Interleukin 1-stimulated Pellino 1 E3 ligase activity but required a relatively high concentration of 10 ⁇ M to achieve complete inhibition (Goh et al., 2011). Sequence alignments do not reveal obvious cysteine residues that could be covalently modified in PIP3K3C, PIP4K2C, and PIP5K3, but further work will be required to evaluate whether these are indeed functional targets of JNK-IN-7.
  • JNK-IN-7 is a relatively selective JNK inhibitor in cells
  • introduction of the “flag” methyl to yield JNK-IN-8 resulted in a dramatic improvement in selectivity and eliminated binding to IRAK1, PIP3K3C, PIP4K2C, and PIP5K3.
  • the dramatic selectivity improvement that results from introduction of this flag-methyl group has been previously reported for imatinib (Zimmermann et al., 1996).
  • Replacement of the pyridine ring with bulkier substituents as exhibited by JNK-IN-11 resulted in a broadening of the selectivity profile as well as further enhancing the potency for inhibition of c-Jun phosphorylation in cells.
  • JNK-IN-11 binds potently to JNKs, p38, PIP5K3, ZAK, ZC2, PIP5K3, and CK1 demonstrating that this compound class might be a valuable lead compound to develop selective inhibitors of these potential alternative targets.
  • JNK-IN-12 bearing a benzothiazol-2-yl acetonitrile moiety, displayed a further broadened profile highlighting the value of KiNativ profiling in evaluating the full spectrum of intracellular targets.
  • JNK-IN-7, JNK-IN-8, and JNK-IN-12 possessed highly selective S scores (defined as the ratio number of kinases inhibited more than 90 percent at screening concentration of 1 ⁇ M) of 0.085, 0.031, and 0.025, respectively ( FIG. 11 ).
  • JNK-IN-7 exhibited binding inhibition of 95% or more to approximately 14 kinases at the concentration of 1.0 ⁇ M. It was attempted to confirm all these potent binding targets using either an enzymatic kinase assay or through the measurement of a dissociation constant to the kinase in question.
  • JNK-IN-7 was confirmed to have a K d or IC 50 of 100 nM or less against eight additional kinases ( FIG. 12 ). JNK-IN-7 was next tested for its ability to inhibit the enzymatic activity of a panel of 121 kinases at a concentration of 1.0 ⁇ M. This analysis revealed 12 kinases that were inhibited more than 80% relative to the DMSO control and follow-up IC 50 determination revealed sub-200 nM IC 50 against of IRAK1, ERK8, and NUAK1 ( FIG. 13 ). JNK-IN-12 bearing a benzothiazol-2-yl acetonitrile in place of the pyridine conferred an improved selectivity relative to JNK-IN-7.
  • the KINOMEscan score for JNK-IN-12 was even smaller than JNK-IN-8, and follow-up enzymatic assays on the potent targets revealed IC 50 's of 37.6, 57.1, and 89.9 nM for IRAK1, HIPK4, and AKT2, respectively ( FIG. 12 ). This high in vitro selectivity however differed markedly from the large number of targets detected by KiNativ.
  • the profiling above provides an assessment of direct engagement with potential targets but does not address further perturbations that maybe induced as a consequence of these binding events.
  • a confocal microscopy-based assay was therefore established using phospho-specific antibodies identical to that used to measure c-Jun phosphorylation, which would report on inhibition phosphorylation of sentinel nodes in other signaling pathways including Erk, p38, JNK, Akt, Stat, NFkB, and Rsk by high throughput microscopy (Table 4 and FIG. 14 ) (Millard, et al., 2011). JNK-IN-7, JNK-IN-8, and JNK-IN-12 exhibited only on-pathway activity as monitored by inhibition of c-Jun phosphorylation.
  • JNK-IN-11 was the only compound found to have off-pathway activity as exemplified by its ability to potently block phosphorylation of ERK, RSK1, MSK1, and p38 consistent with the substantially broadened kinase selectivity profile of this compound. Interestingly, JNK-IN-11 also provided the most complete inhibition of c-Jun phosphorylation which is likely due to its ability to inhibit additional pathways that ultimately signal to phospho-c-Jun.
  • JNK-IN-8 is an efficient, specific, and irreversible intracellular inhibitor of JNK kinase activity by a mechanism that depends on a conserved Cys in the ATP-binding motif.
  • Table 5 demonstrates the dramatic effects changing the orientation of the C and D ring have on JNK activity.
  • “para-meta” compounds of the present invention i.e., compounds comprising para NH groups on phenyl Ring C and meta NH(C ⁇ O) groups on phenyl Ring D
  • “meta-para” compounds comprising meta-NH substituents on phenyl Ring C and para NH(C ⁇ O) groups on phenyl Ring D are surprisingly more active than compounds having the opposite structural configuration, i.e., “meta-para” compounds comprising meta-NH substituents on phenyl Ring C and para NH(C ⁇ O) groups on phenyl Ring D.
  • JNK-IN-7 Molecular docking of JNK-IN-7 into the crystal structures of JNK3, provided a rational basis for structure-guided design of the appropriate linker-element that would serve to connect the phenylaminopyrimidine pharmacophore which is predicted to bind to the kinase-hinge segment with a reactive acrylamide moiety. It was discovered by the inventors of the present invention that the most critical feature to impart potent enzymatic and cellular JNK inhibition was for this linker segment to contain a 1,4-disposition of the dianiline moiety and a 1,3-disposition of terminal aminobenzoic acid moiety as exemplified by JNK-IN-7 and JNK-IN-8.
  • JNK-IN-7 may use a different conformation to recognize these kinases and thereby access an alternative cysteine residue.
  • JNK-IN-7 may form covalent adducts with reactive lysine residues.
  • the natural product inhibitor Wortmannin undergoes a Michael addition reaction with Lys833 of Pi3K, albeit with a different electrophilic moiety. It has been validated that JNK-IN-7 can indeed inhibit IRAK-1 dependent E3 ligase activity of pellino in cells albeit at higher concentrations (1-10 ⁇ M) and further optimization guided by the cell-based assay will be required to establish if more potent cellular inhibition of this target can be achieved (Goh et al., 2011).
  • JNK-IN-7 Two ways were discovered by the inventors of the present invention to further enhance the kinase selectivity of JNK-IN-7.
  • the first was to introduce an ortho-methyl group which is analogous to the “flag” methyl group of imatinib or the ortho-methoxy group of the ALK inhibitor TAE684 (Galkin et al., 2007) and the polo-kinase inhibitor BI-2356 (Kothe et al., 2007).
  • This modification was exemplified by JNK-IN-8, and the crystal structure of JNK-IN-7 predicts that this methyl group could possibly nestle into a small grove along the hinge segment between Asp150 and Ala151 of JNK3.
  • the functionality present in this portion of the inhibitor which is predicted to bind in proximity to the “gatekeeper” methionine provides a critical selectivity determinant for the inhibitors.
  • JNK-IN-11 which possesses a bulky 2-phenylpyrazolo[1,5-a]pyridine group, displays a dramatically broadened inhibition profile in both biochemical and cellular assays.
  • JNK-IN-12 appeared to bind to considerably more kinases based on the KiNativ technology relative to enzymatic or KinomeScan technology. Although there are several non overlapping targets detected by these different technologies, there may be cellular metabolism of the benzothiazol-2-yl acetonitrile moiety to yield species that bind to additional kinase targets. Further work will be required to establish whether the additional targets detected by KiNativ for JNK-IN-7, JNK-IN-11, and JNK-IN-12 are indeed covalently modified and whether bona fide potent cellular inhibition is achieved.
  • Covalent inhibitors are typically designed by rational modification of scaffolds that are already potent non-covalent binders of the desired target protein.
  • the anilinoquinazoline scaffold provides a template for highly potent covalent and non covalent inhibitors of EGFR kinase (Smaill et al., 2000).
  • a second approach is to start from relatively low affinity non-covalent binders and to allow covalent bond formation to drive affinity toward the desired target.
  • the pyrrolopyimidine Rsk inhibitor CMK Cohen et al., 2005
  • the anilinopyrimidine T790M EGFR inhibitor WZ-4002 both gain approximately 100-fold potency for their respective targets by covalent bond formation.
  • the covalent inhibitors described in this study fall into this second category of requiring covalent bond formation in order to achieve potent inhibition of JNK kinase activity.
  • One major advantage of this second approach is that it is much easier to identify a relatively selective low affinity non-covalent scaffold as a starting point relative to a selective high affinity scaffold.
  • the challenge with the second approach is that one has to discover a scaffold that will allow presentation of the electrophile with the ideal geometry to allow for covalent bond formation. This is especially true because the residence time for a low affinity non-covalent compound is typically short.
  • relatively minor changes can have dramatic consequences to the potency of inhibition. This is in sharp contrast to the general notion that a covalent inhibitor will always be exceptionally potent.
  • the first is to generate small rationally designed libraries of electrophile modified inhibitors that can be used in cell-based screens to select for compounds with activity against the desired target.
  • Simple molecular modeling based on known ATP-site recognition modes can be used to select where on the scaffold to modify with an electrophilic group.
  • This approach was used to develop WZ-4002 a potent and selective inhibitor of the T790M “gatekeeper” mutation of EGFR.
  • the disadvantage of this approach is that it requires considerable up-front synthetic effort and the cellular screening approach requires a relatively high efficiency inhibitor be present in the initial screening library.
  • the second approach is to search for low affinity non-covalent scaffolds typically using a biochemical screening approach which allows for screening at high concentrations and then using structure-based drug design to prepare a small library of covalent inhibitors for optimization.
  • the advantage of this approach is that there is large collection of known kinase inhibitors with known kinase selectivity profiles.
  • the disadvantage of this approach is that it can be difficult to predict which scaffold allows for the correct trajectory for the electrophile relative to the protein nucleophile.
  • Use of these and other strategies may provide an efficient means to generate first-in-class covalent inhibitors for the large number of kinases containing suitable cysteine and possibly lysine residues.
  • JNK-IN-8 achieves potent, selective, covalent, and irreversible inhibition of JNK in cells that reaches completion after approximately 3 hours ( FIG. 16 ). It may be recommended that JNK-IN-8 be used at concentrations of approximately 1.0 ⁇ M and that preincubation time be approximately 3 h to inhibit cellular JNK activity.
  • the invention encompasses all variations, combinations, and permutations in which one or more limitations, elements, clauses, and descriptive terms from one or more of the listed claims is introduced into another claim.
  • any claim that is dependent on another claim can be modified to include one or more limitations found in any other claim that is dependent on the same base claim.
  • elements are presented as lists, e.g., in Markush group format, each subgroup of the elements is also disclosed, and any element(s) can be removed from the group. It should it be understood that, in general, where the invention, or aspects of the invention, is/are referred to as comprising particular elements and/or features, certain embodiments of the invention or aspects of the invention consist, or consist essentially of, such elements and/or features.

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